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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 21.2, pp. 507-519
https://doi.org/10.1107/97809553602060000708 Chapter 21.2. Assessing the quality of macromolecular structures
aUnité de Conformation de Macromolécules Biologiques, Université Libre de Bruxelles, avenue F. D. Roosevelt 50, CP160/16, B-1050 Bruxelles, Belgium, and EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England, bUnité de Conformation de Macromolécules Biologiques, Université Libre de Bruxelles, avenue F. D. Roosevelt 50, CP160/16, B-1050 Bruxelles, Belgium, and cDepartment of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA |
References
Abagyan, R. A. & Totrov, M. M. (1997). Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J. Mol. Biol. 268, 678–685.Google Scholar
Agarwal, R. C. (1978). A new least-squares refinement technique based on the fast Fourier transform algorithm. Acta Cryst. A34, 791–809.Google Scholar
Alard, P. (1991). Calcul de surface et d'énergie dans le domaine des macromolécules. PhD thesis dissertation, Université Libre de Bruxelles, Belgium.Google Scholar
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information. Acta Cryst. B35, 2331–2339.Google Scholar
Allen, F. H., Kennard, O. & Taylor, R. (1983). Systematic analysis of structural data as a research technique in organic chemistry. Acc. Chem. Res. 16, 146–153.Google Scholar
Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751–759.Google Scholar
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235–242.Google Scholar
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, 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. J. Mol. Biol. 112, 535–542.Google Scholar
Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K., Westbrook, J. & Fitzgerald, P. M. D. (1997). Macromolecular Crystallographic Information File. Methods Enzymol. 277, 571–590.Google Scholar
Brünger, A. T. (1992a). X-PLOR manual. Version 3.1. New Haven: Yale University Press.Google Scholar
Brünger, A. T. (1992b). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (London), 355, 472–474.Google Scholar
Brünger, A. T. (1997). Free R value: cross-validation in crystallography. Methods Enzymol. 277, 366–396.Google Scholar
Chapman, M. S. (1995). Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Cryst. A51, 69–80.Google Scholar
Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. K. & Berman, H. M. (1996). Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc. 118, 509–518.Google Scholar
Clowney, L., Westbrook, J. D. & Berman, H. M. (1999). CIF applications. XI. A La Mode: a ligand and monomer object data environment. I. Automated construction of mmCIF monomer and ligand models. J. Appl. Cryst. 32, 125–133.Google Scholar
Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.Google Scholar
Cruickshank, D. W. J. (1949). The accuracy of electron-density maps in X-ray analysis with special reference to dibenzyl. Acta Cryst. 2, 65–82.Google Scholar
Cruickshank, D. W. J. (1965). Errors in least-squares methods. In Computing methods in crystallography, edited by J. S. Rollett, pp. 112–116. Oxford: Pergamon Press.Google Scholar
Cruickshank, D. W. J. (1996). Protein precision re-examined: Luzzati plots do not estimate final errors. In Proceedings of the CCP4 study weekend. Macromolecular refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 11–22. Warrington: Daresbury Laboratory.Google Scholar
Das, U., Chen, S., Fuxreiter, M., Vaguine, A. A., Richelle, J., Berman, H. M. & Wodak, S. J. (2001). Checking nucleic acid crystal structures. Acta Cryst. D57, 813–828.Google Scholar
Deacon, A., Gleichmann, T., Kalb (Gilboa), A. J., Price, H., Raftery, J., Bradbrook, G., Yariv, J. & Helliwell, J. R. (1997). The structure of concanavalin A and its bound solvent determined with small-molecule accuracy at 0.94 Å resolution. J. Chem. Soc. Faraday Trans. 93, 4305–4312.Google Scholar
Dodson, E., Kleywegt, G. J. & Wilson, K. (1996). Report of a workshop on the use of statistical validators in protein X-ray crystallography. Acta Cryst. D52, 228–234.Google Scholar
Eisenberg, D., Luthy, R. & Bowie, J. U. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277, 396–404.Google Scholar
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst. A47, 392–400.Google Scholar
EU 3-D Validation Network (1998). Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 276, 417–436.Google Scholar
Finney, J. L. (1975). Volume occupation, environment and accessibility in proteins. The problem of the protein surface. J. Mol. Biol. 96, 721–732.Google Scholar
Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W. K. & Berman, H. M. (1996). Geometric parameters in nucleic acids: sugar and phosphate constituents. J. Am. Chem. Soc. 118, 519–529.Google Scholar
Gellatly, B. J. & Finney, J. L. (1982). Calculation of protein volumes: an alternative to the Voronoi procedure. J. Mol. Biol. 161, 305–322.Google Scholar
Harata, K., Abe, Y. & Muraki, M. (1998). Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion. Proteins, 30, 232–243.Google Scholar
Harpaz, Y., Gerstein, M. & Chothia, C. (1994). Volume changes on protein folding. Structure, 2, 611–649.Google Scholar
Hooft, R. W. W., Sander, C. & Vriend, G. (1996). Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins, 26, 363–376.Google Scholar
Hooft, R. W. W., Sander, C. & Vriend, G. (1997). Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Appl. Biosci. 13, 425–430.Google Scholar
Hooft, R. W. W., Vriend, G., Sander, C. & Abola, E. E. (1996). Errors in protein structures. Nature (London), 381, 272.Google Scholar
Jones, T. A., Zou, J.-Y., Cowan, S. W., Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110–119.Google Scholar
Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577–2637.Google Scholar
Kleywegt, G. J. & Brünger, A. T. (1996). Checking your imagination: applications of the free R value. Structure, 4, 897–904.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1996). Phi/psi-chology: Ramachandran revisited. Structure, 4, 1395–1400.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1998). Databases in protein crystallography. Acta Cryst. D54, 1119–1131.Google Scholar
Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291.Google Scholar
Laskowski, R. A., MacArthur, M. W. & Thornton, J. M. (1998). Validation of protein models derived from experiment. Curr. Opin. Struct. Biol. 8, 631–639.Google Scholar
Longhi, S., Czjzek, M., Lamzin, V., Nicolas, A. & Cambillau, C. (1997). Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: stereochemical analysis. J. Mol. Biol. 268, 779–799.Google Scholar
MacArthur, M. W., Laskowski, R. A. & Thornton, J. M. (1994). Knowledge-based validation of protein-structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr. Opin. Struct. Biol. 4, 731–737.Google Scholar
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., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E. III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D. & Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586–3616.Google Scholar
Melo, F. & Feytmans, E. (1997). Novel knowledge-based mean force potential at atomic level. J. Mol. Biol. 267, 207–222.Google Scholar
Melo, F. & Feytmans, E. (1998). Assessing protein structures with a non-local atomic interaction energy. J. Mol. Biol. 277, 1141–1152.Google Scholar
Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins Struct. Funct. Genet. 12, 345–364.Google Scholar
Murshudov, G. N., Davies, G. J., Isupov, M., Krzywda, S. & Dodson, E. J. (1998). The effect of overall anisotropic scaling in macromolecular refinement. Newsletter on protein crystallography, pp. 37–42. Warrington: Daresbury Laboratory.Google Scholar
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D53, 240–255.Google Scholar
Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Cryst. D52, 57–64.Google Scholar
Pontius, J., Richelle, J. & Wodak, S. J. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. J. Mol. Biol. 264, 121–136.Google Scholar
Ratnaparkhi, G. S., Ramachandran, S., Udgaonkar, J. B. & Varadarajan, R. (1998). Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. Biochemistry, 37, 6958–6966.Google Scholar
Richards, F. M. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1–4.Google Scholar
Richards, F. M. (1985). Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 115, 440–464.Google Scholar
Sayle, R. A. & Milner-White, E. J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20, 374–376.Google Scholar
Schneider, B., Neidle, S. & Berman, H. M. (1997). Conformations of the sugar–phosphate backbone in helical DNA crystal structures. Biopolymers, 42, 113–124.Google Scholar
Sheldrick, G. M. & Schneider, T. R. (1997). SHELXL: high-resolution refinement. Methods Enzymol. 277, 319–343.Google Scholar
Sheriff, S. & Hendrickson, W. A. (1987). Description of overall anisotropy in diffraction from macromolecular crystals. Acta Cryst. A43, 118–121.Google Scholar
Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859–883.Google Scholar
Sippl, M. J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins, 17, 355–362.Google Scholar
Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of γB- and βB2-crystallin. Acta Cryst. D54, 243–252.Google Scholar
Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Cryst. D55, 191–205.Google Scholar
Voronoi, G. F. (1908). Nouvelles applications des paramètres continus à la théorie des formes quadratiques. J. Reine Angew. Math. 134, 198–287.Google Scholar
Walter, R. L., Ealick, S. E., Friedman, A. M., Blake, R. C. II, Proctor, P. & Shoham, M. (1996). Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability. J. Mol. Biol. 263, 730–749.Google Scholar
Wodak, S. J. & Rooman, M. (1993). Generating and testing protein folds. Curr. Opin. Struct. Biol. 3, 247–259.Google Scholar
Zhou, G., Wang, J., Blanc, E. & Chapman, M. S. (1998). Determination of the relative precision of atoms in macromolecular structure. Acta Cryst. D54, 391–399.Google Scholar