Skip to main content Accessibility help

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution

  • Christopher D. Putnam (a1), Michal Hammel (a2), Greg L. Hura (a3) and John A. Tainer (a2) (a4)


Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 Å to 10 Å resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein–nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.


Corresponding author

*Correspondence may be addressed to either author: J. A. Tainer: Tel.: 1 858 784 8119; Fax: 1 858 784 2277; Email:
*G. L. Hura: Tel.: 1 510 486 5378; Fax: 1 510 486 5298; Email:


Hide All
Akiyama, S., Fujisawa, T., Ishimori, K., Morishima, I. & Aono, S. (2004). Activation mechanisms of transcriptional regulator CooA revealed by small-angle X-ray scattering. Journal of Molecular Biology 341, 651668.
Amadei, A., Linssen, A. B. & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins 17, 412425.
Andresen, K., Das, R., Park, H. Y., Smith, H., Kwok, L. W., Lamb, J. S., Kirkland, E. J., Herschlag, D., Finkelstein, K. D. & Pollack, L. (2004). Spatial distribution of competing ions around DNA in solution. Physical Review Letters 93, 248103.
Apic, G., Gough, J. & Teichmann, S. A. (2001). An insight into domain combinations. Bioinformatics 17, S83S89.
Aslam, M., Guthridge, J. M., Hack, B. K., Quigg, R. J., Holers, V. M. & Perkins, S. J. (2003). The extended multidomain solution structures of the complement protein Crry and its chimeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: implications for function and therapy. Journal of Molecular Biology 329, 525550.
Aslam, M. & Perkins, S. J. (2001). Folded-back solution structure of monomeric factor H of human complement by synchrotron X-ray and neutron scattering, analytical ultracentrifugation and constrained molecular modelling. Journal of Molecular Biology 309, 11171138.
Bahadur, R. P., Chakrabarti, P., Rodier, F. & Janin, J. (2004). A dissection of specific and non-specific protein-protein interfaces. Journal of Molecular Biology 336, 943955.
Bahar, I., Atilgan, A. R. & Erman, B. (2001). Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophysical Journal 80, 505515.
Bahattacharyya, R. P., Remenyi, A., Yeh, B. J. & Lim, W. A. (2006). Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuit. Annual Reviews of Biochemistry 75, 655680.
Banci, L., Bertini, I., Gray, H. B., Luchinat, C., Reddig, T., Rosato, A. & Turano, P. (1997). Solution structure of oxidized horse heart cytochrome c. Biochemistry 36, 98679877.
Barrett, C. P. & Noble, M. E. (2005). Dynamite extended: two new services to simplify protein dynamic analysis. Bioinformatics 21, 31743175.
Bax, A. & Grishaev, A. (2005). Weak alignment NMR: a hawk-eyed view of biomolecular structure. Current Opinion in Structural Biology 15, 563570.
Bayburt, T. H., Grinkova, Y. V. & Sligar, S. G. (2006). Assembly of single bacteriorhodopsin trimers in bilayer nanodiscs. Archives of Biochemistry and Biophysics 450, 215222.
Bergmann, A., Fritz, G. & Glatter, O. (2000). Solving the generalized indirect Fourier transformation (GIFT) by Boltzmann simplex simulated annealing (BSSA). Journal of Applied Crystallography 33, 12121216.
Bernado, P., Blanchard, L., Timmins, P., Marion, D., Ruigrok, R. W. & Blackledge, M. (2005). A structural model for unfolded proteins from residual dipolar couplings and small-angle X-ray scattering. Proceedings of the National Academy of Sciences USA 102, 1700217007.
Bernado, P., Mylonas, E., Petoukhov, M. V., Blackledge, M. & Svergun, D. I. (2007). Structural characterization of flexible proteins using small-angle X-ray scattering. Journal of the Americal Chemical Society 129, 56565664.
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology 112, 535542.
Beuron, F., Flynn, T. C., Ma, J., Kondo, H., Zhang, X. & Freemont, P. S. (2003). Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantized elastic deformation model. Journal of Molecular Biology 327, 619629.
Bilgin, N., Ehrenberg, M., Ebel, C., Zaccai, G., Sayers, Z., Koch, M. H., Svergun, D. I., Barberato, C., Volkov, V., Nissen, P. & Nyborg, J. (1998). Solution structure of the ternary complex between aminoacyl-tRNA, elongation factor Tu, and guanosine triphosphate. Biochemistry 37, 81638172.
Binder, K. & Heerman, D. (1992). Monte Carlo Simulation in Statistical Physics, 2nd edn.Berlin: Springer-Verlag.
Bjornson, K. P., Blackwell, L. J., Sage, H., Baitinger, C., Allen, D. & Modrich, P. (2003). Assembly and molecular activities of the MutS tetramer. Journal of Biological Chemistry 278, 3466734673.
Blow, D. M. & Crick, F. H. C. (1959). The treatment of errors in the isomorphous replacement method. Acta Crystallographica 12, 794802.
Blundell, T. L. & Johnson, L. N. (1976). Protein Crystallography. London: Academic Press.
Bochtler, M., Hartmann, C., Song, H. K., Bourenkov, G. P., Bartunik, H. D. & Huber, R. (2000). The structures of HslU and the ATP-dependent protease HslU-HslV. Nature 403, 800805.
Boehm, M. K., Woof, J. M., Kerr, M. A. & Perkins, S. J. (1999). The Fab and Fc fragments of IgA1 exhibit a different arrangement from that in IgG: a study by X-ray and neutron solution scattering and homology modelling. Journal of Molecular Biology 286, 14211447.
Boehr, D. D., McElheny, D., Dyson, H. J. & Wright, P. E. (2006). The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 16381642.
Bonvin, A. M. (2006). Flexible protein-protein docking. Current Opinions in Structural Biology 16, 194200.
Borgstahl, G. E., Parge, H. E., Hickey, M. J., Johnson, M. J., Boissinot, M., Hallewell, R. A., Lepock, J. R., Cabelli, D. E. & Tainer, J. A. (1996). Human mitochondrial manganese superoxide dismutase polymorphic variant Ile58Thr reduces activity by destabilizing the tetrameric interface. Biochemistry 35, 42874297.
Boskovic, J., Rivera-Calzada, A., Maman, J. D., Chacon, P., Willison, K. R., Pearl, L. H. & Llorca, O. (2003). Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs. EMBO Journal 22, 58755882.
Bourne, Y., Arvai, A. S., Bernstein, S. L., Watson, M. H., Reed, S. I., Endicott, J. E., Noble, M. E., Johnson, L. N. & Tainer, J. A. (1995). Crystal structure of the cell cycle-regulatory protein suc1 reveals a beta-hinge conformational switch. Proceedings of the National Academy of Sciences USA 92, 1023210236.
Bourne, Y., Redford, S. M., Steinman, H. M., Lepock, J. R., Tainer, J. A. & Getzoff, E. D. (1996). Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase. Proceedings of the National Academy of Sciences USA 93, 1277412779.
Brooks, B. & Karplus, M. (1985). Normal modes for specific motions of macromolecules: applications to the hinge-bending mode of lysozyme. Proceedings of the National Academy of Sciences USA 82, 49954999.
Brudler, R., Gessner, C. R., Li, S., Tyndall, S., Getzoff, E. D. & Woods, V. L. Jr. (2006). PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry. Journal of Molecular Biology 363, 148160.
Brulet, A., Boue, F. & Cotton, J. P. (1996). About the experimental determination of the persistence length of wormlike chains of polystyrene. Journal of Physics II (France) 6, 855891.
Brunger, A. T. (1992). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472475.
Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kuntsleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallographica D54, 905921.
Brunger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science 235, 458460.
Brunner-Popela, J. & Glatter, O. (1997). Small-angle scattering of interacting particles. I. Basic principles of a global evaluation technique. Journal of Applied Crystallography 30, 431442.
Bu, Z. & Engelman, D. M. (1999). A method for determining transmembrane helix association and orientation in detergent micelles using small angle x-ray scattering. Biophysical Journal 77, 10641073.
Buey, R. M., Monterroso, B., Menendez, M., Diakun, G., Chacon, P., Hermoso, J. A. & Diaz, J. F. (2007). Insights into molecular plasticity of choline binding proteins (Pneumococcal surface proteins) by SAXS. Journal of Molecular Biology 365, 411424.
Burmeister, W. P. (2000). Structural changes in a cryo-cooled protein crystal owing to radiation damage. Acta Crystallographica D56, 328341.
Caffrey, M. (2000). A lipid's eye view of membrane protein crystallization in mesophases. Current Opinions in Structural Biology 10, 486497.
Calmettes, P., Durand, D., Desmadril, M., Minard, P., Receveur, V. & Smith, J. C. (1994). How random is a highly denatured protein? Biophysical Chemistry 53, 105114.
Canady, M. A., Tsuruta, H. & Johnson, J. E. (2001). Analysis of rapid, large-scale protein quaternary structure changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NΩV) maturation. Journal of Molecular Biology 311, 803814.
Chacon, P., Diaz, J. F., Moran, F. & Andreu, J. M. (2000). Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. Journal of Molecular Biology 299, 12891302.
Chacon, P., Moran, F., Diaz, F. J., Pantos, E. & Andreu, J. M. (1998). Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophysical Journal 74, 27602775.
Chacon, P., Tama, F. & Wriggers, W. (2003). Mega-dalton biomolecular motion captured from electron microscopy reconstructions. Journal of Molecular Biology 326, 485492.
Chacon, P. & Wriggers, W. (2002). Multi-resolution contour-based fitting of macromolecular structures. Journal of Molecular Biology 317, 375384.
Chamberlain, A. K., Receveur, V., Spencer, A., Redfield, C. & Dobson, C. M. (2001). Characterization of the structure and dynamics of amyloidogenic variants of human lysozyme by NMR spectroscopy. Protein Science 10, 25252530.
Chapados, B. R., Hosfield, D. J., Han, S., Qiu, J., Yelent, B., Shen, B. & Tainer, J. A. (2004). Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116, 3950.
Chen, B., Doucleff, M., Wemmer, D. E., De Carlo, S., Huang, H. H., Nogales, E., Hoover, T. R., Kondrashkina, E., Guo, L. & Nixon, B. T. (2007). ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, σ54. Structure 15, 429440.
Chen, L., Hodgson, K. O. & Doniach, S. (1996). A lysozyme folding intermediate revealed by solution X-ray scattering. Journal of Molecular Biology 261, 658671.
Chen, R., Li, L. & Weng, Z. (2003). ZDOCK: an initial-stage protein-docking algorithm. Proteins 52, 8087.
Columbus, L., Lipfert, J., Klock, H., Millett, I., Doniach, S. & Lesley, S. A. (2006). Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination. Protein Science 15, 961975.
Corn, J. E., Pease, P. J., Hura, G. L. & Berger, J. M. (2005). Crosstalk between primase subunits can act to regulate primer synthesis in trans. Molecular Cell 20, 391401.
Cowtan, K. & Main, P. (1996). Phase combination and cross validation in iterated density-modification calculations. Acta Crystallographica D52, 4348.
Cowtan, K. & Main, P. (1998). Miscellaneous algorithms for density modifications. Acta Crystallographica D54, 487493.
Craig, L., Volkmann, N., Arvai, A. S., Pique, M. E., Yeager, M., Egelman, E. H. & Tainer, J. A. (2006). Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Molecular Cell 23, 651662.
D'Arcy, A. (1994). Crystallizing proteins – a rational approach? Acta Crystallographica D50, 469471.
Dainese, E., Sabatucci, A., van Zadelhoff, G., Angelucci, C. B., Vachette, P., Veldink, G. A., Agro, A. F. & Maccarrone, M. (2005). Structural stability of soybean lipoxygenase-1 in solution as probed by small angle X-ray scattering. Journal of Molecular Biology 349, 143152.
Dauter, Z. (1997). Data collection strategy. Methods in Enzymology 276, 326344.
Davies, J. M., Tsuruta, H., May, A. P. & Weis, W. I. (2005). Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-ray scattering. Structure 13, 183195.
Delarue, M. & Dumas, P. (2004). On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proceedings of the National Academy of Sciences USA 101, 69576962.
Deng, H.-X., Hentai, A., Tainer, J. A., Iqbal, Z., Cayabyab, A., Hung, W.-Y., Getzoff, E. D., Herzfeldt, B., Roos, R. P., Warner, C., Deng, G., Soriano, E., Smyth, C., Parge, H. E., Ahmed, A., Roses, A. D., Hallewell, R. A., Pericak-Vance, M. A. & Siddique, T. (1993). Amyotropic lateral sclerosis and structural defects in Cu,Zn superoxide dismutase. Science 261, 10471051.
Denisov, I. G., Grinkova, Y. V., Lazarides, A. A. & Sligar, S. G. (2004). Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size. Journal of the American Chemical Society 126, 34773487.
dePristo, M. A., de Bakker, P. I. & Blundell, T. L. (2004). Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure 12, 831838.
DiDonato, M., Craig, L., Huff, M. E., Thayer, M. M., Cardoso, R. M., Kassmann, C. J., Lo, T. P., Bruns, C. K., Powers, E. T., Kelly, J. W., Getzoff, E. D. & Tainer, J. A. (2003). ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization. Journal of Molecular Biology 332, 601615.
Diederichs, K., Diez, J., Greller, G., Mueller, C., Breed, J., Schnell, C., Vornrhein, C., Boos, W. & Welte, W. (2000). Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis. EMBO Journal 19, 59515961.
Dominguez, C., Bonvin, A. M., Winkler, G. S., van Schaik, F. M., Timmers, H. T. & Boelens, R. (2004). Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure 12, 633644.
Doniach, S. (2001). Changes in biomolecular conformation seen by small angle X-ray scattering. Chemical Reviews 101, 17631778.
Dore, A. S., Kilkenny, M. L., Jones, S. A., Oliver, A. W., Roe, S. M., Bell, S. D. & Pearl, L. H. (2006). Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity. Nucleic Acids Research 34, 45154526.
Doublie, S. (1997). Preparation of selenometionyl proteins for phase determination. Methods in Enzymology 276, 523530.
Drenth, J. (1994). Principles of Protein X-ray Crystallography. New York: Springer-Verlag.
Drotschmann, K., Aronshtam, A., Fritz, H.-J. & Marinus, M. G. (1998). The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA. Nucleic Acids Research 26, 948953.
Dubochet, J., Adrian, M., Chang, J. J., Homo, J. C., Lepault, J., McDowall, A. W. & Schultz, P. (1988). Cryo-electron microscopy of vitrified specimens. Quarterly Reviews in Biophysics 21, 129228.
Dyson, H. J. & Wright, P. E. (2005). Intrinsically unstructured proteins and their functions. Nature Reviews of Molecular Cell Biology 6, 197208.
Echols, N., Milburn, D. & Gerstein, M. (2003). MolMovDB: analysis and visulation of conformational change and structural flexibility. Nucleic Acids Research 31, 478482.
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallographica A47, 392400.
Evans, S. K. & Lundblad, V. (1999). Est1 and Cdc13 as comediators of telomerase access. Science 286, 117120.
Fang, X., Littrell, K., Yang, X. J., Henderson, S. J., Siefert, S., Thiyagarajan, P., Pan, T. & Sosnick, T. R. (2000). Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 39, 1110711113.
Faure, P., Micu, A., Perahia, D., Doucet, J., Smith, J. C. & Benoit, J. P. (1994). Correlated intramolecular motions and diffuse X-ray scattering in lysozyme. Nature Stuctural Biology 1, 124128.
Ferre-D'Amare, A. R. & Burley, S. K. (1997). Dynamic light scattering in evaluating crystallizability of macromolecules. Methods in Enzymology 276, 157166.
Ferreira da Silva, F., Pereira, P. J., Gales, L., Roessle, M., Svergun, D. I., Moradas-Ferreira, P. & Damas, A. M. (2006). The crystal structure and solution structures of glyceraldehyde-3-phosphate dehydrogenase reveal different quaternary structures. Journal of Biological Chemistry 281, 3343333440.
Fetler, L., Tauc, P., Herve, G., Moody, M. F. & Vachette, P. (1995). X-ray scattering titration of the quaternary structure transition of aspartate transcarbamylase with a bisubstrate analogue: influence of nucleotide effectors. Journal of Molecular Biology 251, 243255.
Filgueira de Azevedo, W. Jr., dos Santos, G. C., dos Santos, D. M., Olivieri, J. R., Canduri, F., Silva, R. G., Basso, L. A., Renard, G., da Fonseca, I. O., Mendes, M. A., Palma, M. S. & Santos, D. S. (2003). Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase. Biochemical and Biophysical Research Communications 309, 923928.
Foster, B. A., Coffey, H. A., Morin, M. J. & Rastinejad, F. (1999). Pharmacological rescue of mutant p53 conformation and function. Science 286, 25072510.
Fowler, A. G., Foote, A. M., Moody, M. F., Vachette, P., Provencher, S. W., Gabriel, A., Bordas, J. & Koch, M. H. (1983). Stopped-flow solution scattering using synchrotron radiation: apparatus, data collection and data analysis. Journal of Biochemical and Biophysical Methods 7, 317329.
Franklin, R. E. & Gosling, R. G. (1953a). Evidence for 2-chain helix in crystalline structure of sodium deoxyribonucleate. Nature 172, 156157.
Franklin, R. E. & Gosling, R. G. (1953b). Molecular configuration in sodium thymonucleate. Nature 421, 400401.
Fraser, R. D. B., MacRae, T. P. & Suzuki, E. (1978). An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules. Journal of Applied Crystallography 11, 693694.
Fujisawa, T., Uruga, T., Yamaizumi, Z., Inoko, Y., Nishimura, S. & Ueki, T. (1994). The hydration of Ras p21 in solution during GTP hydrolysis based on solution X-ray scattering profile. Journal of Biochemistry (Tokyo) 115, 875880.
Furnham, N., Blundell, T. L., DePristo, M. A. & Terwilliger, T. C. (2006). Is one solution good enough? Nature Stuctural Biology 13, 184185.
Gallagher, S. C., Callaghan, A. J., Zhao, J., Dalton, H. & Trewhella, J. (1999). Global conformational changes control the reactivity of methane monooxygenase. Biochemistry 38, 67526760.
Garman, E. F. & Schneider, T. R. (1997). Macromolecular crystallography. Journal of Applied Crystallography 30, 211237.
Getzoff, E. D., Tainer, J. A. & Olson, A. J. (1986). Recognition and interactions controlling the assemblies of beta barrel domains. Biophysical Journal 49, 191200.
Gherardi, E., Sandin, S., Petoukhov, M. V., Finch, J., Youles, M. E., Ofverstedt, L. G., Miguel, R. N., Blundell, T. L., Vande Woude, G. F., Skoglund, U. & Svergun, D. I. (2006). Structural basis of hepatocyte growth factor/scatter factor and MET signalling. Proceedings of the National Academy of Sciences USA 103, 40464051.
Giacovazzo, C., Monaco, H. L., Viterbo, D., Scordari, F., Gilli, G., Zanotti, G. & Catti, M. (1992). Fundamentals of Crystallography. Oxford: Oxford University Press.
Gilbert, H. E., Asokan, R., Holers, V. M. & Perkins, S. J. (2006). The 15 SCR flexible extracellular domains of human complement receptor type 2 can mediate multiple ligand and antigen interactions. Journal of Molecular Biology 362, 11321147.
Gilbert, H. E., Eaton, J. T., Hannan, J. P., Holers, V. M. & Perkins, S. J. (2005). Solution structure of the complex between CR2 SCR 1–2 and C3d of human complement: an X-ray scattering and sedimentation modeling study. Journal of Molecular Biology 346, 859873.
Gillmor, S. A., Villasenor, A., Fletterick, R., Sigal, E. & Browner, M. F. (1997). The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity. Nature Stuctural Biology 4, 10031009.
Glatter, O. (1977). A new method for the evaluation of small angle X-ray scattering data. Journal of Applied Crystallography 10, 415421.
Glatter, O. (1982). Data treatment. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 120165. London: Academic Press.
Goettig, P., Brandstetter, H., Groll, M., Gohring, W., Konarev, P. V., Svergun, D. I., Huber, R. & Kim, J. S. (2005). X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum. Journal of Biological Chemistry 280, 3338733396.
Graille, M., Zhou, C.-Z., Receveur-Brechot, V., Collinet, B., Declerck, N. & van Tileurgh, H. (2005). Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. Journal of Biological Chemistry 280, 1478014789.
Grishaev, A., Wu, J., Trewhella, J. & Bax, A. (2005). Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data. Journal of the American Chemical Society 127, 1662116628.
Grossmann, J. G., Abraham, Z. H., Adman, E. T., Neu, M., Eady, R. R., Smith, B. E. & Hasnain, S. S. (1993). X-ray scattering using synchrotron radiation shows nitrite reductase from Achromobacter xylosoxidans to be a trimer in solution. Biochemistry 32, 73607366.
Guarne, A., Ramon-Maiques, S., Wolff, E. M., Ghirlando, R., Hu, X., Miller, J. H. & Yang, W. (2004). Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair. EMBO Journal 23, 41344145.
Guinier, A. & Fournet, F. (1955). Small Angle Scattering of X-rays. New York: Wiley Interscience
Gutberlet, T., Heinemann, U. & Steiner, M. (2001). Protein crystallography with neutrons – status and perspectives. Acta Crystallographica D57, 349354.
Habel, J. E., Ohren, J. F. & Borgstahl, G. E. O. (2001). Dynamic light-scattering analysis of full-length human RPA14/32 dimer: purification, crystallization and self-association. Acta Crystallographica D57, 254259.
Hamada, D., Higurashi, T., Mayangi, K., Miyata, T., Fukui, T., Iida, T., Honda, T. & Yanagihara, I. (2007). Tetrameric structure of the thermostable direct hemolysin from Vibrio parahaemolyticus revealed by ultracentrifugation, small-angle X-ray scattering and electron microscopy. Journal of Molecular Biology 365, 187195.
Hammel, M., Fierobe, H. P., Czjzek, M., Finet, S. & Receveur-Brechot, V. (2004a). Structural insights into the mechanism of formation of cellulosomes probed by small angle X-ray scattering. Journal of Biological Chemistry 279, 5598555994.
Hammel, M., Fierobe, H. P., Czjzek, M., Kurkal, V., Smith, J. C., Bayer, E. A., Finet, S. & Receveur-Brechot, V. (2005). Structural basis of cellulosome efficiency explored by small angle X-ray scattering. Journal of Biological Chemistry 280, 3856238568.
Hammel, M., Kriechbaum, M., Gries, A., Kostner, G. M., Laggner, P. & Prassl, R. (2002). Solution structure of human and bovine β(2)-glycoprotein I revealed by small-angle X-ray scattering. Journal of Molecular Biology 321, 8597.
Hammel, M., Sfyroera, G., Ricklin, D., Magotti, P., Lambris, J. D. & Geisbrecht, B. V. (2007). A structural basis for complement inhibition by Staphylococcus aureus. Nature Immunology 8, 430437.
Hammel, M., Walther, M., Prassl, R. & Kuhn, H. (2004b). Structural flexibility of the N-terminal beta-barrel domain of 15-lipoxygenase-1 probed by small angle X-ray scattering. Functional consequences for activity regulation and membrane binding. Journal of Molecular Biology 343, 917929.
Hansmann, U. H. E. & Okamoto, Y. (1999). New Monte Carlo algorithms for protein folding. Current Opinions in Structural Biology 9, 177183.
Hao, Q. (2001). Phasing from an envelope. Acta Crystallographica D57, 14101414.
Hao, Q. (2006). Macromolecular envelope determination and envelope-based phasing. Acta Crystallographica D62, 909914.
Hao, Q., Dodd, F. E., Grossmann, J. G. & Hasnain, S. S. (1999). Ab initio phasing using molecular envelopes from solution X-ray scattering. Acta Crystallographica D55, 243246.
Head-Gordon, T. & Hura, G. (2002). Water structure from scattering experiments and simulation. Chemical Reviews 102, 26512670.
Heifetz, A. & Eisenstein, M. (2003). Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking. Protein Engineering 16, 179–85.
Heller, W. T. (2005). Influence of multiple well-defined conformations on small-angle scattering of proteins in solution. Acta Crystallographica D61, 3344.
Heller, W. T. (2006). ELLSTAT: shape modeling for solution small-angle scattering of proteins and protein complexes with automated statistical characterization. Journal of Applied Crystallography 39, 671675.
Heller, W. T., Krueger, J. K. & Trewhella, J. (2003). Further insights into calmodulin-myosin light chain kinase interaction from solution scattering and shape restoration. Biochemistry 42, 1057910588.
Helliwell, J. R. (1997). Overview of synchrotron radiation and macromolecular crystallography. Methods in Enzymology 276, 203217.
Hendrickson, W. A. & Ogata, C. M. (1997). Phase determination from multiwavelength anomalous diffraction measurements. Methods in Enzymology 276, 494523.
Hess, M. T., Gupta, R. D. & Kolodner, R. D. (2002). Dominant Saccharomyces cerevisiae msh6 mutations cause increased mispair binding and decreased disassociation from mispairs by Msh2-Msh6 in the absence of ATP. Journal of Biological Chemistry 277, 2554525553.
Hinsen, K. (1998). Analysis of domain motions by approximate normal mode calculations. Proteins 33, 417429.
Hinsen, K., Reuter, N., Navaza, J., Stokes, D. L. & Lacapere, J. J. (2005). Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophysical Journal 88, 818827.
Hope, H. (1990). Crystallography of biological macromolecules at ultra-low temperature. Annual Reviews of Biophysics and Biophysical Chemistry 19, 107126.
Hopfner, K. P., Karcher, A., Craig, L., Woo, T. T., Carney, J. P. & Tainer, J. A. (2001). Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell 105, 473485.
Hopfner, K. P., Karcher, A., Shin, D. S., Craig, L., Arthur, L. M., Carney, J. P. & Tainer, J. A. (2000). Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily. Cell 101, 789800.
Howlin, B., Butler, S. A., Moss, D. S., Harris, G. W. & Driessen, H. P. C. (1993). TLSANL: TLS parameter-analysis program for segmented anisotropic refinement of macromolecular structures. Journal of Applied Crystallography 26, 622.
Hubbard, S. R., Hodgson, K. O. & Doniach, S. (1988). Small-angle X-ray scattering investigation of the solution structure of troponin C. Journal of Biological Chemistry 263, 41514158.
Hung, L.-W., Wang, I. X., Nikaido, K., Liu, P.-Q., Ames, G. F. & Kim, S.-H. (1998). Crystal structure of the ATP-binding subunit of an ABC transporter. Nature 396, 703707.
Jancarik, J., Pufan, R., Hong, C., Kim, S.-H. & Kim, R. (2004). Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins. Acta Crystallographica D60, 16701673.
Jelsch, C., Teeter, M. M., Lamzin, V., Pichon-Pesme, V., Blessing, R. H. & Lecomte, C. (2000). Accurate protein crystallography at ultrahigh resolution: valence electron distribution in crambin. Proceedings of the National Academy of Sciences USA 97, 31713176.
Johs, A., Hammel, M., Waldner, I., May, R. P., Laggner, P. & Prassl, R. (2006). Modular structure of solubilized human apolipoprotein B-100. Low resolution model revealed by small angle neutron scattering. Journal of Biological Chemistry 281, 1973219739.
Jones, P. M. & George, A. M. (1999). Subunit interactions in ABC transporters: toward a functional architecture. FEMS Microbiology Letters 179, 187202.
Jones, S. & Thornton, J. M. (1996). Principles of protein-protein interactions. Proceedings of the National Academy of Sciences USA 93, 1320.
Kamata, K., Mitsuya, M., Nishimura, T., Eiki, J. & Nagata, Y. (2004). Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase. Structure 12, 429438.
Karplus, M. & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Stuctural Biology 9, 646652.
Karpowich, N., Martsinkevich, O., Millen, L., Yuan, Y.-R., Dia, P. L., MacVey, K., Thomas, P. J. & Hunt, J. F. (2001). Crystal structure of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter. Structure 9, 571586.
Ke, H. (1997). Overview of isomorphous replacement phasing. Methods in Enzymology 276, 448461.
Keskin, O., Ma, B. & Nussinov, R. (2005). Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. Journal of Molecular Biology 345, 12811294.
Kidera, A. & Go, N. (1990). Refinement of protein dynamic structure: normal mode refinement. Proceedings of the National Academy of Sciences USA 87, 37183722.
Kleywegt, G. J. & Jones, T. A. (1997). Model building and refinement practice. Methods in Enzymology 277, 208230.
Knablein, J., Neuefeind, T., Schneider, F., Bergner, A., Messerschmidt, A., Lowe, J., Steipe, B. & Huber, R. (1997). Ta6Br(2+)12, a tool for phase determination of large biological assemblies by X-ray crystallography. Journal of Molecular Biology 270, 17.
Ko, T. P., Robinson, H., Gao, Y. G., Cheng, C. H., DeVries, A. L. & Wang, A. H. (2003). The refined crystal structure of an eel type III antifreeze protein RD1 at 0·62 Å resolution reveals structural microheterogeneity of protein and solvation. Biophysical Journal 84, 12281237.
Koch, M. H., Vachette, P. & Svergun, D. I. (2003). Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Quarterly Reviews of Biophysics 36, 147227.
Kollman, J. M. & Quispe, J. (2005). The 17 A structure of the 420 kDa lobster clottable protein by single particle reconstruction from cryoelectron micrographs. Journal of Structural Biology 151, 306314.
Konarev, P. V., Petoukhov, M. V. & Svergun, D. I. (2001). MASSHA – a graphics system for rigid-body modeling of macromolecular complexes against solution scattering data. Journal of Applied Crystallography 34, 527532.
Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J. & Svergun, D. I. (2003). PRIMUS: a Windows PC-based system for small-angle scattering data analysis. Journal of Applied Crystallography 36, 12771282.
Kong, Y., Ming, D., Wu, Y., Stoops, J. K., Zhou, Z. H. & Ma, J. (2003). Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model. Journal of Molecular Biology 330, 129135.
Kontopidis, G., Wu, S. Y., Zheleva, D. I., Taylor, P., McInnes, C., Lane, D. P., Fischer, P. M. & Walkinshaw, M. D. (2005). Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design. Proceedings of the National Academy of Sciences USA 102, 18711876.
Korzhnev, D. M., Billeter, M., Arseniev, A. S. & Orekhov, V. Y. (2001). NMR studies of Brownian tumbling and internal motions in proteins. Progress Nuclear Magnetic Resonance Spectroscopy 38, 197266.
Kosinski, J., Steindorf, L., Bujnicki, J. M., Giron-Monzon, L. & Friedhoff, P. (2005). Analysis of the quaternary structure of the MutL C-terminal domain. Journal of Molecular Biology 351, 895909.
Kozak, M. (2005). Direct comparison of the crystal and solution structure of glucose/xylose isomerase from Streptomyces rubiginosus. Protein Peptide Letters 12, 547550.
Kozin, M. B. & Svergun, D. I. (2001). Automated matching of high- and low-resolution structural models. Journal of Applied Crystallography 34, 3341.
Kozin, M. B., Volkov, V. V. & Svergun, D. I. (1997). ASSA, a program for three-dimensional rendering in solution scattering from biopolymers. Journal of Applied Crystallography 30, 811815.
Kratky, O. & Porod, G. (1949). Roetgenuntersuchung Geloester Fadenmolekuele. Recueil des Travaux Chimiques des Pays-Bas 68, 11061122.
Krebs, A., Durchschlag, H. & Zipper, P. (2004). Small angle X-ray scattering studies and modeling of Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin. Biophysical Journal 87, 11731185.
Krebs, W. G., Alexandrov, V., WIlson, C. A., Echols, N., Yu, H. & Gerstein, M. (2002). Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48, 682695.
Kuhn, L. A., Siani, M. A., Pique, M. E., Fisher, C. L., Getzoff, E. D. & Tainer, J. A. (1992). The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. Journal of Molecular Biology 228, 1322.
Kuwamoto, S., Akiyama, S. & Fujisawa, T. (2004). Radiation damage to a protein solution, detected by synchrotron X-ray small-angle scattering: dose-related considerations and suppression by cryoprotectants. Journal of Synchrotron Radiation 11, 462468.
Kwok, L. W., Shcherbakova, I., Lamb, J. S., Park, H. Y., Andresen, K., Smith, H., Brenowitz, M. & Pollack, L. (2006). Concordant exploration of the kinetics of RNA folding from global and local perspectives. Journal of Molecular Biology 355, 282293.
Lamers, M. H., Georgescu, R. E., Lee, S. G., O'Donnell, M. & Kuriyan, J. (2006). Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III. Cell 126, 881892.
Lamers, M. H., Georgijevic, D., Lebbink, J. H., Winterwerp, H. H. K., Agianian, B., de Wind, N. & Sixma, T. K. (2004). ATP increases the affinity between MutS ATPase domains: Implications for ATP hydrolysis and conformational changes. Journal of Biological Chemistry 279, 4387943885.
Lamers, M. H., Perrakis, A., Enzlin, J. H., Winterwerp, H. H., de Wind, N. & Sixma, T. K. (2000). The crystal structure of the DNA mismatch repair protein MutS binding to a G×T mismatch. Nature 407, 711717.
Lattman, E. E. (1989). Rapid calculation of the solution scattering profile from a macromolecule of known structure. Proteins 5, 149155.
Leach, A. R. (2001). Exploring conformational space using simulation methods. In Molecular Modelling: Principles and Applications (ed. Hall, P.), pp. 457508. Harlow: Pearson Education.
Lee, K. K., Gan, L., Tsuruta, H., Hendrix, R. W., Duda, R. L. & Johnson, J. E. (2004). Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid. Journal of Molecular Biology 340, 419433.
Lei, M., Zavodszky, M. I., Kuhn, L. A. & Thorpe, M. F. (2004). Sampling protein conformations and pathways. Journal of Computational Chemistry 25, 11331148.
Levitt, M., Sander, C. & Stern, P. S. (1985). Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease, and lysozyme. Journal of Molecular Biology 181, 423447.
Levy, Y. & Becker, O. M. (2002). Conformational polymorphism of wild-type and mutant prion proteins: energy landscape analysis. Proteins 47, 458468.
Li, L., Chen, R. & Weng, Z. (2003). RDOCK: refinement of rigid-body protein docking predictions. Proteins 53, 693707.
Li, X., Keskin, O., Ma, B., Nussinov, R. & Liang, J. (1985). Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that preorganize in the unbound states: implications for docking. Journal of Molecular Biology 334, 781795.
Lindahl, E. & Delarue, M. (2005). Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimiziation. Nucleic Acids Research 33, 44964506.
Lipfert, J., Columbus, L., Chu, V. B. & Doniach, S. (2007a). Analysis of small-angle X-ray scattering data of protein-detergent complexes by singular value decomposition. Journal of Applied Crystallography 40, 15.
Lipfert, J., Das, R., Chu, V. B., Kudaravalli, M., Boyd, N., Herschlag, D. & Doniach, S. (2007b). Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology 365, 13931406.
Lipfert, J. & Doniach, S. (2007). Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annual Review of Biophysics and Biomolecular Structure 36, 307327.
Liu, Q., Weaver, A. J., Xiang, T., Thiel, D. J. & Hao, Q. (2003). Low-resolution molecular replacement using a six-dimensional search. Acta Crystallographica D59, 10161019.
Locher, K. P., Lee, A. T. & Rees, D. C. (2002). The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 296, 10911098.
Losonczi, J. A., Andrec, M., Fischer, M. W. & Prestegard, J. H. (1999). Order matrix analysis of residual dipolar couplings using singular value decomposition. Journal of Magnetic Resonance 138, 334342.
Lucic, V., Forster, F. & Baumeister, W. (2005). Structural studies by electron tomography: from cells to molecules. Annual Reviews in Biochemistry 74, 833865.
Lunde, C. S., Rouhani, S., Facciotti, M. T. & Glaeser, R. M. (2006). Membrane-protein stability in a phospholipid-based crystallization medium. Journal of Structural Biology 154, 223231.
Ma, B., Elkayam, T., Wolfson, H. & Nussinov, R. (2003). Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proceedings of the National Academy of Sciences USA 100, 57725777.
MacKerell, A. D. Jr., Bashford, D., Bellott, M., Dunbrack, R. L. Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Mischnick, S., Ngo, T., Nguygen, D. T., Prodhom, B., Reiher, W. E. III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Staub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. & Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102, 35863616.
Maiorov, V. & Abagyan, R. (1997). A new method for modeling large-scale rearrangements of protein domains. Proteins 27, 410424.
Mandell, J. G., Roberts, V. A., Pique, M. E., Kotlovyi, V., Mitchell, J. C., Nelson, F., Tsigelny, I. & Ten Eyck, L. F. (2001). Protein docking using continuum electrostatics and geometric fit. Protein Engineering 14, 105113.
Marino, M., Zou, P., Svergun, D., Garcia, P., Edlich, C., Simon, B., Wilmanns, M., Muhle-Goll, C. & Mayans, O. (2006). The Ig doublet Z1Z2: a model system for the hybrid analysis of conformational dynamics in Ig tandems from titin. Structure 14, 14371447.
Matthews, B. W. (1968). Solvent content of protein crystals. Journal of Molecular Biology 33, 491497.
Mattinen, M. L., Paakkonen, K., Ikonen, T., Craven, J., Drakenberg, T., Serimaa, R., Waltho, J. & Annila, A. (2002). Quaternary structure built from subunits combining NMR and small-angle X-ray scattering data. Biophysical Journal 83, 11771183.
McMurray, C. T. & Tainer, J. A. (2003). Cancer, cadmium and genome integrity. Nature Genetics 34, 239241.
Meinhold, L. & Smith, J. C. (2007). Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins Structure Function and Bioinformatics 66, 941953.
Mendenhall, M. D. & Hodge, A. F. (1998). Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae. Microbial Molecular Biology Reviews 62, 11911243.
Mendillo, M. L., Mazur, D. J. & Kolodner, R. D. (2005). Analysis of the interaction between the Saccharomyces cerevisiae MSH2-MSH6 and MLH1-PMS1 complexes with DNA using a reversible DNA end-blocking system. Journal of Biological Chemistry 280, 2224522257.
Mendillo, M. L., Putnam, C. D. & Kolodner, R. D. (2007). Escherichia coli MutS tetramerization domain structure reveals that stable dimers but not tetramers are essential for DNA mismatch repair in vivo. Journal of Biological Chemistry 282, 1634516354.
Merzel, F. & Smith, J. C. (2002a). Is the first hydration shell of lysozyme of higher density than bulk water? Proceedings of the National Academy of Sciences USA 99, 53785383.
Merzel, F. & Smith, J. C. (2002b). SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallographica D58, 242249.
Metropolis, N., Rosenbluth, A., Rosenbluth, M., Teller, A. & Teller, E. (1953). Equation of state calculations by fast computing machines. Journal of Chemical Physics 21, 10871092.
Miake-Lye, R. C., Doniach, S. & Hodgson, K. O. (1983). Anomalous x-ray scattering from terbium-labeled parvalbumin in solution. Biophysical Journal 41, 287292.
Mitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks, C. L. 3rd, Ban, N. & Frank, J. (2005). Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438, 318324.
Mizuguchi, K., Kidera, A. & Go, N. (1994). Collective motions in proteins investigated by X-ray diffuse scattering. Proteins 18, 3448.
Montange, R. K. & Batey, R. T. (2006). Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441, 11721175.
Moore, P. B. (1980). Small-angle scattering. Information content and error analysis. Journal of Applied Crystallography 13, 168175.
Mueller, J. J., Hansen, S. & Puerschel, H. V. (1996). The use of small-angle scattering and the maximum-entropy method for shape-model determination from distance-distribution functions. Journal of Applied Crystallography 29, 547554.
Muller, K., Laggner, P., Glatter, O. & Kostner, G. (1978). The structure of human-plasma low-density lipoprotein B. An X-ray small-angle scattering study. European Journal of Biochemistry 82, 7390.
Mustard, D. & Ritchie, D. W. (2005). Docking essential dynamics eigenstructures. Proteins 60, 269274.
Mylonas, F. & Svergun, D. I. (2007). Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering. Journal of Applied Crystallography 40, s245s249.
Nagar, B., Hantschel, O., Seeliger, M., Davies, J. M., Weis, W. I., Superti-Furga, G. & Kuriyan, J. (2006). Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase. Molecular Cell 21, 787798.
Nagar, B., Hantschel, O., Young, M. A., Scheffzek, K., Veach, D., Bornmann, W., Clarkson, B., Superti-Furga, G. & Kuriyan, J. (2003). Structural basis of the autoinhibition of c-Abl tyrosine kinase. Cell 112, 859871.
Nath, A., Atkins, W. M. & Sligar, S. G. (2007). Applications of phospholipid bilayer nanodiscs in the study of membranes and membrane proteins. Biochemistry 46, 20592069.
Navaza, J. (2001). Implementation of molecular replacement in AMoRe. Acta Crystallographica D57, 13671372.
Navaza, J., Lepault, J., Rey, F. A., Alvarez-Rua, C. & Borge, J. (2002). On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation. Acta Crystallographica D58, 18201825.
Nemeth-Pongracz, V., Barabas, O., Fuxreiter, M., Simon, I., Pichova, I., Rumlova, M., Zabranska, H., Svergun, D., Petoukhov, M., Harmat, V., Klement, E., Hunyadi-Gulyas, E., Medzihradszky, K. F., Konya, E. & Vertessy, B. G. (2007). Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins. Nucleic Acids Research 35, 495505.
Nilsson, L., Clore, G. M., Gronenbom, A. M., Brunger, A. T. & Karplus, M. (1986). Structural refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton restrains: application to 5′d(C-G-T-A-C-G)2. Journal of Molecular Biology 188, 455475.
Nowak, E., Panjikar, S., Konarev, P., Svergun, D. I. & Tucker, P. A. (2006a). The structural basis of signal transduction for the response regulator PrrA from Mycobacterium tuberculosis. Journal of Biological Chemistry 281, 96599666.
Nowak, E., Panjikar, S., Morth, J. P., Jordanova, R., Svergun, D. I. & Tucker, P. A. (2006b). Structural and functional aspects of the sensor histidine kinase PrrB from Mycobacterium tuberculosis. Structure 14, 275285.
Obmolova, G., Ban, C., Hsieh, P. & Yang, W. (2000). Crystal structure of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407, 703710.
Ockwell, D. M., Hough, M., Grossmann, J. G., Hasnain, S. S. & Hao, Q. (2000). Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering. Acta Crystallographica D56, 10021006.
Palma, P. N., Krippahl, L., Wampler, J. E. & Moura, J. J. (2000). BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins 39, 372384.
Parge, H. E., Arvai, A. S., Murtari, D. J., Reed, S. I. & Tainer, J. A. (1993). Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control. Science 262, 387395.
Parsiegla, G., Reverbel-Leroy, C., Tardif, C., Belaich, J. P., Driguez, H. & Haser, R. (2000). Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action. Biochemistry 39, 1123811246.
Pascal, J. M., O’Brien, P. J., Tomkinson, A. E. & Ellenberger, T. (2004). Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432, 473478.
Pascal, J. M., Tsodikov, O. V., Hura, G. L., Song, W., Cotner, E. A., Classen, S., Tomkinson, A. E., Tainer, J. A. & Ellenberger, T. (2006). A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Molecular Cell 24, 279291.
Pennock, E., Buckley, K. & Lundblad, V. (2001). Cdc13 delivers separate complexes to the telomere for end protection and replication. Cell 104, 387396.
Perez, J., Vachette, P., Russo, D., Desmadril, M. & Durand, D. (2001). Heat-induced unfolding of neocarzinostatin, a small all-beta protein investigated by small-angle X-ray scattering. Journal of Molecular Biology 308, 721743.
Perkins, S. J. (2001). X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and modeling fits. Biophysical Chemistry 93, 129139.
Perrakis, A., Morris, R. M. & Lamzin, V. S. (1999). Automated protein model building combined with iterative structure refinement. Nature Stuctural Biology 6, 458463.
Perry, J. J., Fan, L. & Tainer, J. A. (2007). Developing master keys to brain pathology, cancer, and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair. Neuroscience 145, 12801299.
Perry, J. J., Yannone, S. M., Holden, L. G., Hitomi, C., Asaithamby, A., Han, S., Cooper, P. K., Chen, D. J. & Tainer, J. A. (2006). WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nature Strucutral and Molecular Biology 13, 414422.
Perutz, M. F., Bolton, W., Diamond, R., Muirhead, H. & Watson, H. C. (1964). Structure of haemoglobin. An X-ray examination of reduced horse haemoglobin. Nature 203, 687690.
Petoukhov, M. V., Eady, N. A., Brown, K. A. & Svergun, D. I. (2002). Addition of missing loops and domains to protein models by X-ray solution scattering. Biophysical Journal 83, 31133125.
Petoukhov, M. V., Monie, T. P., Allain, F. H., Matthews, S., Curry, S. & Svergun, D. I. (2006). Conformation of polypyrimidine tract binding protein in solution. Structure 14, 10211027.
Petoukhov, M. V. & Svergun, D. I. (2005). Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophysical Journal 89, 12371250.
Petoukhov, M. V. & Svergun, D. I. (2006). Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution. European Biophysical Journal 35, 567576.
Petoukhov, M. V., Svergun, D. I., Konarev, P. V., Ravasio, S., van den Heuvel, R. H., Curti, B. & Vanoni, M. A. (2003). Quaternary structure of Azospirillum brasilense NADPH-dependent glutamate synthase in solution as revealed by synchrotron radiation x-ray scattering. Journal of Biological Chemistry 278, 2993329939.
Petrova, T. & Podjarny, A. (2004). Protein crystallography at subatomic resolution. Reports on Progress in Physics 67, 15651605.
Pilz, I. (1982). Proteins. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 239293. London: Academic Press.
Pioletti, M., Findeisen, F., Hura, G. L. & Minor, D. L. J. (2006). Three-dimensional structure of KChIP1-Kv4.3 T1 complex reveals a cross-shaped octamer. Nature Strucutral and Molecular Biology 13, 987995.
Porod, G. (1951). X-ray small angle scattering of close packed colloidal systems. Kolloid Zeitschrift 124, 83114.
Porod, G. (1982). General Theory. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 1751. London: Academic Press.
Press, W. H., Teukolsky, S. A., Vetterling, W. T. & Flannery, B. P. (1992). Numerical Recipes in C, Second Edition. New York, NY: Cambridge University Press
Provencher, S. W. & Glockner, J. (1983). Analysis of the components present in kinetics (or titration) curves. Journal of Biochemical and Biophysical Methods 7, 331334.
Putnam, C. D., Clancy, S. B., Tsuruta, H., Gonzalez, S., Wetmur, J. G. & Tainer, J. A. (2001). Structure and mechanism of the RuvB Holliday junction branch migration motor. Journal of Molecular Biology 311, 297310.
Putnam, C. D., Shroyer, M. J., Lundquist, A. J., Mol, C. D., Arvai, A. S., Mosbaugh, D. W. & Tainer, J. A. (1999). Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase. Journal of Molecular Biology 287, 331346.
Putnam, C. D. & Tainer, J. A. (2005). Protein mimicry of DNA and pathway regulation. DNA Repair 4, 14101420.
Qazi, O., Bolgiano, B., Crane, D., Svergun, D. I., Konarev, P. V., Yao, Z. P., Robinson, C. V., Brown, K. A. & Fairweather, N. (2007). The HC fragment of tetanus toxin forms stable, concentration-dependent dimers via an intermolecular disulphide bond. Journal of Molecular Biology 365, 123134.
Rajamani, D., Thiel, S., Vajda, S. & Camacho, C. J. (2004). Anchor residues in protein-protein interactions. Proceedings of the National Academy of Sciences USA 101, 1128711292.
Rallison, J. M. & Harding, S. E. (1985). Excluded volume for pairs of triaxial ellipsoids at dominant Brownian motion. Journal of Colloid Interface Science 103, 284289.
Ravelli, R. B. & McSweeney, S. M. (2000). The ‘fingerprint’ that X-rays can leave on structures. Structure Fold Design 8, 315328.
Redecke, L., Bergen, M., Clos, J., Konarev, P. V., Svergun, D. I., Fittschen, U. E., Broekaert, J. A., Bruns, O., Georgieva, D., Mandelkow, E., Genov, N. & Betzel, C. (2007). Structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro. Journal of Structural Biology 157, 308320.
Rejto, P. A. & Freer, S. T. (1996). Protein conformational substrates from X-ray crystallography. Progress in Biophysical and Molecular Biology 66, 167196.
Rodier, F., Bahadur, R. P., Chakrabarti, P. & Janin, J. (2005). Hydration of protein-protein interfaces. Proteins 60, 3645.
Roseman, A. M. (2000). Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallographica D56, 13321340.
Rosenberg, O. S., Deindl, S., Sung, R. J., Nairn, A. C. & Kuriyan, J. (2005). Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme. Cell 123, 849860.
Rossmann, M. G. (1995). Ab initio phase determination and phase extension using non-crystallographic symmetry. Current Opinions in Structural Biology 5, 650655.
Rossmann, M. G. (2000). Fitting atomic models into electron-microscopy maps. Acta Crystallographica D56, 13411349.
Rouiller, I., DeLaBarre, B., May, A. P., Weis, W. I., Brunger, A. T., Milligan, R. A. & Wilson-Kubalek, E. M. (2002). Conformational changes of the multifunctional p97 AAA ATPase during its ATPase cycle. Nature Structural Biology 9, 950957.
Sakurai, S., Kitano, K., Yamaguchi, H., Hamada, K., Okada, K., Fukuda, K., Uchida, M., Ohtsuka, E., Morioka, H. & Hakoshima, T. (2005). Structural basis for recruitment of human flap endonuclease 1 to PCNA. EMBO Journal 34, 683693.
Sanishvili, R., Volz, K. W., Westbrook, E. M. & Margoliash, E. (1995). The low ionic strength crystal structure of horse cytochrome c at 2·1 Å resolution and comparison with its high ionic strength counterpart. Structure 3, 707716.
Scheres, S. H. G., H. Valle, M., Herman, G. T., Eggermont, P. P., Frank, J. & Carazo, J. M. (2007). Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nature Methods 4, 2729.
Schlick, T. (2001). Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work. Structure 9, R4553.
Schnecke, V., Swanson, C. A., Getzoff, E. D., Tainer, J. A. & Kuhn, L. A. (1998). Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins 33, 7487.
Schomaker, V. & Trueblood, K. (1968). On rigid body motion of molecules in crystals. Acta Crystallographica B24, 6376.
Semenyuk, A. V. & Svergun, D. I. (1991). GNOM – a program package for small-angle scattering data processing. Journal of Applied Crystallography 24, 537540.
Shannon, C. E. & Moore, W. (1949). The Mathematical Theory of Communication. Urbana, IL: University of Illinois Press.
Sheldrick, G. M. & Schneider, T. R. (1997). SHELXL: high-resolution refinement. Methods in Enzymology 277, 319343.
Shell, S. S., Putnam, C. D. & Kolodner, R. D. (2007). The N terminus of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA. Molecular Cell 26, 565578.
Shin, D. S., Pellegrini, L., Daniels, D. S., Yelent, B., Craig, L., Bates, D., Yu, D. S., Shivji, M. K., Hitomi, C., Arvai, A. S., Volkmann, N., Tsuruta, H., Blundell, T. L., Venkitaraman, A. R. & Tainer, J. A. (2003). Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO Journal. 22, 45664576.
Sim, G. A. (1959). The distribution of phase angles for structrues containing heavy atoms. II. A modification of the normal heavy atom method for non-centrosymmetric structures. Acta Crystallographica 12, 813815.
Smith, G. R., Sternberg, M. J. & Bates, P. A. (2005). The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. Journal of Molecular Biology 347, 10771101.
Smith, K. F., Harrison, R. A. & Perkins, S. J. (1990). Structural comparisons of the native and reactive-centre-cleaved forms of alpha 1-antitrypsin by neutron- and X-ray scattering in solution. Biochemical Journal 267, 203212.
Smith, P. E., van Schaik, R. C., Szyperski, T., Wuthrich, K. & van Gunsteren, W. F. (1995). Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. Journal of Molecular Biology 246, 356365.
Sokolova, A. V., Volkov, V. V. & Svergun, D. I. (2003a). Database for rapid protein classification based on small-angle X-ray scattering data. Crystallography Reports 48, 10271033.
Sokolova, A. V., Volkov, V. V. & Svergun, D. I. (2003b). Prototype of a database for rapid protein classification based on solution scattering data. Journal of Applied Crystallography 36, 865868.
Sondermann, H., Nagar, B., Bar-Sagi, D. & Kuriyan, J. (2005). Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless. Proceedings of the National Academy of Sciences USA 102, 1663216637.
Sousa, M. C., Trame, C. B., Tsuruta, H., Wilbanks, S. M., Reddy, V. S. & McKay, D. B. (2000). Crystal and solution structures of an HslUV protease-chaperone complex. Cell 103, 633643.
Stuhrmann, H. B. (1973). Comparison of the three basic scattering functions of myoglobin in solution with those from the known structure in crystalline state. Journal of Molecular Biology 77, 363369.
Stuhrmann, H. B. (1981). Anomalous small angle scattering. Quarterly Reviews in Biophysics 14, 433460.
Stuhrmann, H. B. (1982). Contrast variation. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 197213. London: Academic Press.
Stuhrmann, H. B., Haas, J., Ibel, K., Wolf, B., Koch, M. H., Parfait, R. & Crichton, R. R. (1976). New low resolution model for 50S subunit of Escherichia coli ribosomes. Proceedings of the National Academy of Sciences USA 73, 2379–83.
Stuhrmann, H. B., Tardieu, A., Mateu, L., Sardet, C., Luzzati, V., Aggerbeck, L. & Scanu, A. M. (1975). Neutron scattering study of human serum low density lipoprotein. Proceedings of the National Academy of Sciences USA 72, 22702273.
Suhre, K., Navaza, J. & Sanejouand, Y. H. (2006). NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallographica D62, 10981100.
Suhre, K. & Sanejouand, Y. H. (2004). ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research 32, W610614.
Sun, Z., Reid, K. B. & Perkins, S. J. (2004). The dimeric and trimeric solution structures of the multidomain complement protein properdin by X-ray scattering, analytical ultracentrifugation and constrained modeling. Journal of Molecular Biology 343, 13271343.
Svergun, D. (1992). Determination of the regularization parameter in indirect-transform methods using perceptual criteria. Journal of Applied Crystallography 25, 495503.
Svergun, D., Baraberato, C. & Koch, M. H. (1995). CRYSOL – a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. Journal of Applied Crystallography 28, 768773.
Svergun, D. I. (1999). Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophysical Journal 76, 28792886.
Svergun, D. I. (2007). Small-angle scattering studies of macromolecular solutions. Journal of Applied Crystallography 40, s10s17.
Svergun, D. I., Burkhardt, N., Pedersen, J. S., Koch, M. H., Volkov, V. V., Kozin, M. B., Meerwink, W., Stuhrmann, H. B., Diedrich, G. & Nierhaus, K. H. (1997a). Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. I. Invariants and validation of electron microscopy models. Journal of Molecular Biology 271, 588601.
Svergun, D. I., Burkhardt, N., Pedersen, J. S., Koch, M. H., Volkov, V. V., Kozin, M. B., Meerwink, W., Stuhrmann, H. B., Diedrich, G. & Nierhaus, K. H. (1997b). Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. II. A model of the ribosome and its RNA at 3·5 nm resolution. Journal of Molecular Biology 271, 602618.
Svergun, D. I., Petoukhov, M. V. & Koch, M. H. (2001a). Determination of domain structure of proteins from X-ray solution scattering. Biophysical Journal 80, 29462953.
Svergun, D. I., Petoukhov, M. V. & Koch, M. H. (2001b). Determination of domain structure of proteins from X-ray solution scattering. Biophysical Journal 76, 28792886.
Svergun, D. I., Petoukhov, M. V., Koch, M. H. J. & Koenig, S. (2000). Crystal versus solution structures of thiamine diphosphate-dependent enzymes. Journal of Biological Chemistry 275, 297302.
Svergun, D. I. & Stuhrmann, H. B. (1991). New developments in direct shape determination from small-angle scattering. 1. Theory and model calculations. Acta Crystallographica A47, 736744.
Svergun, D. I., Volkov, V. V., Kozin, M. B. & Stuhrmann, H. B. (1996). New developments in direct shape determination from small-angle scattering. 2. Uniqueness. Acta Crystallographica A52, 419426.
Tai, K. (2004). Conformational sampling for the impatient. Biophysical Chemistry 107, 213220.
Takahashi, Y., Nishikawa, Y. & Fujisawa, T. (2003). Evaluation of three algorithms for ab initio determination of three dimensional shapes from one dimensional solvent scattering profiles. Journal of Applied Crystallography 36, 546550.
Tama, F., Miyashita, O. & Brooks, C. L. 3rd (2004). Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. Journal of Molecular Biology 337, 985999.
Tama, F. & Sanejouand, Y. H. (2001). Conformational change of proteins arising from normal mode analysis. Protein Engineering 14, 16.
Tama, F., Wriggers, W. & Brooks, C. L. 3rd (2002). Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. Journal of Molecular Biology 321, 297305.
Taylor, A., Dunne, M., Bennington, S., Ansell, S., Gardner, I., Norreys, P., Broome, T., Findlay, D. & Nelmes, R. (2007). A route to the brightest possible neutron source? Science 317, 10921095.
Terwilliger, T. C. (2003). Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallographica D59, 3844.
Tidow, H., Melero, R., Mylonas, E., Freund, S. M. V., Grossmann, J. G., Carazo, J. M., Svergun, D. I., Valle, M. & Fersht, A. R. (2007). Quaternary structures of tumor suppressor p53 and a specific p53-DNA complex. Proceedings of the National Academy of Sciences USA 104, 1232412329.
Tiede, D. M., Zhang, R. & Seifert, S. (2002). Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C. Biochemistry 41, 66056614.
Tiede, D. M. & Zuo, X. (2007). X-ray scattering for bio-molecule structure characterization. In Biophysical Techniques in Photosynthesis II (ed. Aartsma, T. J. and Matysik, J.). Springer.
Tirion, M. M. (1996). Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Physical Review Letters 77, 19051908.
Tjioe, E. & Heller, W. T. (2007). ORNL_SAS: software for calculation of small-angle scattering intensities of proteins and protein complexes. Journal of Applied Crystallography 40, 782785.
Trikha, J., Theil, E. C. & Allewell, N. M. (1995). High resolution structure of amphibian red-cell L-ferritin: potential roles for structural plasticity and solvation in function. Journal of Molecular Biology 248, 949967.
Tsutakawa, S. E., Hura, G. L., Frankel, K. A., Cooper, P. K. & Tainer, J. A. (2007). Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography. Journal of Structural Biology 158, 214223.
Tung, C. S., Walsh, D. A. & Trewhella, J. (2002). A structural model of the catalytic subunit-regulatory subunit dimeric complex of the cAMP-dependent protein kinase. Journal of Biological Chemistry 277, 1242312431.
Urzhumtsev, A. G. & Podjarny, A. (1995). On the solution of the molecular-replacement problem at very low resolution: application to large complexes. Acta Crystallographica D51, 888895.
Uzawa, T., Kimura, T., Ishimori, K., Morishima, I., Matsui, T., Ikeda-Saito, M., Takahashi, S., Akiyama, S. & Fujisawa, T. (2006). Time-resolved small-angle X-ray scattering investigation of the folding dynamics of heme oxygenase: implication of the scaling relationship for the submillisecond intermediates of protein folding. Journal of Molecular Biology 357, 9971008.
Vachette, P. & Svergun, D. (2000). Small-angle X-ray scattering by solutions of biological macromolecules: neutron and synchrotron radiation for condensed studies. In Structure and Dynamics of Biomolecules (ed. Fanchon, E., Geissler, E., Hodeau, J. L., Regnard, J. E. and Timmins, P. A.), pp. 199237. Oxford: Oxford University Press.
Valdar, W. S. & Thornton, J. M. (2001a). Conservation helps to identify biologically relevant crystal contacts. Journal of Molecular Biology 313, 399416.
Valdar, W. S. & Thornton, J. M. (2001b). Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 42, 108124.
van Aalten, D. M., Conn, D. A., de Groot, B. L., Berendsen, H. J., Findlay, J. B. & Amadei, A. (1997). Protein dynamics derived from clusters of crystal structures. Biophysical Journal 73, 28912896.
Vellieux, F. M. D. & Read, R. J. (1997). Non-crystallographic symmetry averaging in phase refinement and extension. Methods in Enzymology 277, 1853.
Vestergaard, B. & Hansen, S. (2006). Application of Bayesian analysis to indirect Fourier transformation in small-angle scattering. Journal of Applied Crystallography 39, 797804.
Vestergaard, B., Sanyal, S., Roessle, M., Mora, L., Buckingham, R. H., Kastrup, J. S., Gajhede, M., Svergun, D. I. & Ehrenberg, M. (2005). The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure. Molecular Cell 20, 929938.
Volkmann, N. & Hanein, D. (1999). Quantitative fitting of atomic models into observed densities derived by electron microscopy. Journal of Structural Biology 125, 176184.
Volkmann, N. & Hanein, D. (2003). Docking of atomic models into reconstructions from electron microscopy. Methods Enzymol 374, 204225.
Volkov, V. V. & Svergun, D. I. (2003). Uniqueness of ab initio shape determination in small-angle scattering. Journal of Applied Crystallography 36, 860864.
von Ossowski, I., Eaton, J. T., Czjzek, M., Perkins, S. J., Frandsen, T. P., Schulein, M., Panine, P., Henrissat, B. & Receveur-Brechot, V. (2005). Protein disorder: conformational distribution of the flexible linker in a chimeric double cellulase. Biophysical Journal 88, 28232832.
Vucetic, S., Brown, C. J., Dunker, A. K. & Obradovic, Z. (2003). Flavors of protein disorder. Proteins 52, 573584.
Wall, M. E., Clarage, J. B. & Phillips, G. N. (1997a). Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 5, 15991612.
Wall, M. E., Ealick, S. E. & Gruner, S. M. (1997b). Three-dimensional diffuse X-ray scattering from crystals of Staphylococcal nuclease. Proceedings of the National Academy of Sciences USA 94, 61806184.
Wall, M. E., Gallagher, S. C. & Trewhella, J. (2000). Large-scale shape changes in proteins and macromolecular complexes. Annual Review of Physcial Chemistry 51, 355380.
Walther, D., Cohen, F. E. & Doniach, S. (2000). Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray solution scattering data for biomolecules. Journal of Applied Crystallography 33, 350363.
Weber, P. C. (1997). Overview of protein crystallization methods. Methods in Enzymology 276, 1322.
Weeks, C. M., Blessing, R. H., Miller, R., Mungee, R., Potter, S. A., Rappleye, J., Smith, G. D., Xu, H. & Furey, W. (2002). Toward automated protein structure determination: BnP, the SnB-PHASES interface. Zeitschrift fur Kristallographie 217, 686693.
Williams, R. S., Chasman, D. I., Hau, D. D., Hui, B., Lau, A. Y. & Glover, J. N. (2003). Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. Journal of Biological Chemistry 278, 5300753016.
Willis, B. T. M. & Pryor, A. W. (1975). Thermal Vibrations in Crystallography. London: Cambridge University Press.
Wilson, A. J. C. (1942). Determination of absolute from relative X-ray intensity data. Nature 150, 152.
Wilson, M. A. & Brunger, A. T. (2000). The 1·0 Å crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. Journal of Molecular Biology 301, 12371256.
Winn, M. D., Isupov, M. N. & Murshudov, G. N. (2001). Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallographica D57, 122133.
Winn, M. D., Murshudov, G. N. & Papiz, M. Z. (2003). Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods in Enzymology 374, 300321.
Wriggers, W. & Chacon, P. (2001). Modeling tricks and fitting techniques for multiresolution structures. Structure 9, 779788.
Wriggers, W., Milligan, R. A. & McCammon, J. A. (1999). Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. Journal of Structural Biology 125, 185195.
Wu, L. & Hickson, I. D. (2006). DNA helicases required for homologous recombination and repair of damaged replication forks. Annual Review of Genetics 40, 279306.
Yamagata, A. & Tainer, J. A. (2007). Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. EMBO Journal 26, 878890.
Yeats, T. O. (1997). Detecting and overcoming crystal twinning. Methods in Enzymology 276, 344358.
Yuan, Y.-R., Blecker, S., Martsinkevich, O., Millen, Y., Thomas, P. J. & Hunt, J. F. (2001). The crystal structure of the MJ0796 ATP-binding cassette: implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter. Journal of Biological Chemistry 276, 3231332321.
Yuzawa, S., Yokochi, M., Hatanaka, H., Ogura, K., Kataoka, M., Miura, K., Mandiyan, V., Schlessinger, J. & Inagaki, F. (2001). Solution structure of Grb2 reveals extensive flexibility necessary for target recognition. Journal of Molecular Biology 306, 527537.
Zegerman, P. & Diffley, J. F. X. (2007). Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature 445, 281285.
Zhang, K. Y. J., Cowtan, K. & Main, P. (1997). Combining constraints for electron density modification. Methods in Enzymology 277, 5364.
Zhang, R., Thiyagarajan, P. & Tiede, D. M. (2000a). Probing protein fine structures by wide angle solution X-ray scattering. Journal of Applied Crystallography 33, 565568.
Zhang, X., Shaw, A., Bates, P. A., Newman, R. H., Bowen, B., Orlova, E., Gorman, M. A., Kondo, H., Dokurno, P. & Lally, J. (2000b). Structure of the AAA ATPase p97. Molecular Cell 6, 14731484.
Zhao, J., Hoye, E., Boylan, S., Walsh, D. A. & Trewhella, J. (1998). Quaternary structure of a catalytic subunit-regulatory subunit dimeric complex and the holoenzyme of the cAMP-dependent protein kinase by neutron contrast variation. Journal of Biological Chemistry 273, 3044830459.
Zheng, Y., Doerschuk, P. C. & Johnson, J. E. (1995). Determination of three-dimensional low-resolution viral structure from solution X-ray scattering. Biophysical Journal 69, 619639.
Zipper, P. & Durschschlag, H. (2003). Modeling of protein solution structures. Journal of Applied Crystallography 36, 509514.
Zuker, M., Mathews, D. H. & Turner, D. H. (1999). Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology. Dordrecht: Kluwer Academic Publishers.
Zulauf, M. & D'Arcy, A. (1992). Light scattering of proteins as a criterion for crystallization. Journal of Crystal Growth 122, 102106.