Abstract
This chapter discusses two important aspects of the structure determination process that are related to the accuracy and reliability of the crystallographic model under investigation. Quality control is defined as the analysis of an intermediate model to identify aspects of it that are unusual in some sense and that could, therefore, be a result of errors in the model building or refinement process. Any such errors need to be fixed, if at all possible, prior to analysis and publication of the model. Validation is the process of assessing the reliability of the final model (or certain aspects of it, e.g., the active site residues) that is about to be analyzed, published, deposited, and possibly used in follow-up studies.
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References
Brändén, C. I. and Jones, T. A. (1990) Between objectivity and subjectivity. Nature 343, 687–689.
Kleywegt, G. J. and Jones, T. A. (1995) Where freedom is given, liberties are taken. Structure 3, 535–540.
Kleywegt, G. J. (2000) Validation of protein crystal structures. Acta Crystallogr. D56, 249–265.
Davis, A. M., Teague, S. J., and Kleywegt, G. J. (2003) Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem. Int. Ed. 42, 2718–2736.
Kleywegt, G. J., Henrick, K., Dodson, E. J., and van Aalten, D. M. F. (2003) Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement? Structure 11, 1051–1059.
Kleywegt, G. J. and Hansson, H. (2005) Retrieval and validation of structural information. In: Structural Genomics and High Throughput Structural Biology (Sundström, M., Norin, M., and Edwards, A., eds.), Taylor and Francis, Boca Raton, FL, pp. 185–222.
MacArthur, M. W., Laskowski, R. A., and 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.
Zou, J. Y. and Mowbray, S. L. (1994) An evaluation of the use of databases in protein structure refinement. Acta Crystallogr. D50, 237–249.
Kleywegt, G. J. and Jones, T. A. (1995) Braille for pugilists. In: Making the Most of Your Model, (Hunter, W. N., Thornton, J. M., and Bailey, S., eds.), SERC Daresbury Laboratory, Warrington, UK, pp. 11–24.
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.
Laskowski, R. A., MacArthur, M. W., and Thornton, J. M. (1998) Validation of protein models derived from experiment. Curr. Opin. Struct. Biol. 8, 631–639.
Laskowski, R. A. (2003) Structural quality assurance. In: Structural Bioinformatics, (Bourne, P. E. and Weissig, H., eds.), Wiley-Liss, Hoboken, NJ, pp. 273–303.
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.
Berman, H. M., Westbrook, J., Feng, Z., et al. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235–242.
Collaborative Computational Project, Nr. 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763.
Hooft, R. W. W., Vriend, G., Sander, C. and Abola, E. E. (1996) Errors in protein structures. Nature 381, 272–272.
Kleywegt, G. J. and Jones, T. A. (1996) xdlMAPMAN and xdlDATAMAN-programs for reformatting, analysis and manipulation of biomacromolecular electrondensity maps and reflection data sets. Acta Crystallogr. D52, 826–828.
Kleywegt, G. J. and Jones, T. A. (1996) Efficient rebuilding of protein structures. Acta Crystallogr. D52, 829–832.
Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110–119.
Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240–255.
Potterton, E., Briggs, P., Turkenburg, M., and Dodson, E. (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr. D59, 1131–1137.
Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140–149.
Kleywegt, G. J., Harris, M. R., Zou, J. Y., Taylor, T. C., Wählby, A., and Jones, T. A. (2004) The Uppsala electron-density server. Acta Crystallogr. D60, 2240–2249.
Kleywegt, G. J. and Read, R. J. (1997) Not your average density. Structure 5, 1557–1569.
Bhat, T. N. (1988) Calculation of an OMIT map. J. Appl. Crystallogr. 21, 279–281.
Hodel, A., Kim, S. H., and Brünger, A. T. (1992) Model bias in macromolecular crystal structures. Acta Crystallogr. A48, 851–858.
Vellieux, F. M. D. and Dijkstra, B. W. (1997) Computation of Bhat’s OMIT map with different coefficients. J. Appl. Crystallogr. 30, 396–399.
Vriend, G. and Sander, C. (1993) Quality control of protein models: directional atomic contact analysis. J. Appl. Crystallogr. 26, 47–60.
Hooft, R. W. W., Sander, C., and Vriend, G. (1996) Verification of protein structures: side-chain planarity. J. Appl. Crystallogr. 29, 714–716.
Hooft, R. W. W., Sander, C. and Vriend, G. (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Applic. Biosci. 13, 425–430.
Kleywegt, G. J. and Jones, T. A. (1998) Databases in protein crystallography. Acta Crystallogr. D54, 1119–1131.
Jones, T. A. and Kjeldgaard, M. (1997) Electron density map interpretation. Methods Enzymol. 277, 173–208.
Kleywegt, G. J. and Jones, T. A. (1997) Model-building and refinement practice. Methods Enzymol. 277, 208–230.
Brünger, A. T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–475.
Kleywegt, G. J. and Brünger, A. T. (1996) Checking your imagination: applications of the free R value. Structure 4, 897–904.
Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291.
Kleywegt, G. J. and Jones, T. A. (1996) Phi/Psi-chology: Ramachandran revisited. Structure 4, 1395–1400.
Lovell, S. C., Davis, I. W., Arendall, W. B., 3rd, et al. (2003) Structure validation by Cα geometry: σ,ψ and Cβ deviation. Proteins Struct. Funct. Genet. 50, 437–450.
Eisenberg, D., Lüthy, R., and Bowie, J. U. (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277, 396–404.
Dym, O., Eisenberg, D., and Yeates, T. O. (2001) Detection of errors in protein models. In: International Tables for Crystallography. Volume F. Crystallography of Biological Macromolecules (Rossmann, M.G. and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 520–525.
Kleywegt, G. J. (1996) Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D52, 842–857.
Kleywegt, G. J. (1999) Experimental assessment of differences between related protein crystal structures. Acta Crystallogr. D55, 1878–1884.
Engh, R. A. and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A47, 392–400.
Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T., and Berman, H. M. (1996) New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr. D52, 57–64.
Engh, R. A. and Huber, R. (2001) Structure quality and target parameters. in International Tables for Crystallography. Volume F. Crystallography of Biological Macromolecules, (Rossmann, M. G., and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 382–392.
Jones, T. A., Kleywegt, G. J. and Brünger, A. T. (1996) Storing diffraction data. Nature 381, 18–19.
Brünger, A. T., Kuriyan, J., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics. Science 235, 458–460.
Brünger, A. T., Adams, P. D., Clore, G. M., et al. (1998) Crystallography and NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905–921.
Tronrud, D. E. (1997) The TNT refinement package. Methods Enzymol. 277, 306–319.
McRee, D. E. (1999) XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165.
Sheldrick, G. M. and Schneider, T. R. (1997) SHELXL: high-resolution refinement. Methods Enzymol. 277, 319–344.
Van den Akker, F. and Hol, W. G. J. (1999) Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structures. Acta Crystallogr. D55, 206–218.
Colovos, C. and Yeates, T. O. (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Prot. Sci. 2, 1511–1519.
Kleywegt, G. J., Zou, J. Y., Kjeldgaard, M., and Jones, T. A. (2002) Around O. International Tables for Crystallography, Volume F, Crystallography of Biological Macromolecules (Rossmann, M. G. and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 353–367.
Das, U., Chen, S., Fuxreiter, M., et al. (2001) Checking nucleic acid crystal structures. Acta Crystallogr. D57, 813–828.
Jones, T. A. (1978) A graphics model building and refinement system for macromolecules. J. Appl. Crystallogr. 11, 268–272.
Oldfield, T. J. (2001) A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. Acta Crystallogr. D57, 82–94.
Vaguine, A. A., Richelle, J., and 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 Crystallogr. D55, 191–205.
Zou, J. Y. and Jones, T. A. (1996) Towards the automatic interpretation of macromolecular electron-density maps: qualitative and quantitative matching of protein sequence to map. Acta Crystallogr. D52, 833–841.
Jones, T. A. and Liljas, L. (1984) Crystallographic refinement of macromolecules having non-crystallographic symmetry. Acta Crystallogr. A40, 50–57.
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Kleywegt, G.J. (2007). Quality Control and Validation. In: Doublié, S. (eds) Macromolecular Crystallography Protocols. Methods in Molecular Biology™, vol 364. Humana Press. https://doi.org/10.1385/1-59745-266-1:255
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DOI: https://doi.org/10.1385/1-59745-266-1:255
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