Macromolecular Crystallography Protocols pp 255-272

Part of the Methods in Molecular Biology™ book series (MIMB, volume 364)

Quality Control and Validation

  • Gerard J. Kleywegt
Protocol

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.

Key Words

Electron density model bias model building protein structure quality control Ramachandran plot refinement structure validation X-ray crystallography 

References

  1. 1.
    Brändén, C. I. and Jones, T. A. (1990) Between objectivity and subjectivity. Nature 343, 687–689.CrossRefGoogle Scholar
  2. 2.
    Kleywegt, G. J. and Jones, T. A. (1995) Where freedom is given, liberties are taken. Structure 3, 535–540.PubMedCrossRefGoogle Scholar
  3. 3.
    Kleywegt, G. J. (2000) Validation of protein crystal structures. Acta Crystallogr. D56, 249–265.Google Scholar
  4. 4.
    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.CrossRefGoogle Scholar
  5. 5.
    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.PubMedCrossRefGoogle Scholar
  6. 6.
    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.CrossRefGoogle Scholar
  7. 7.
    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.CrossRefGoogle Scholar
  8. 8.
    Zou, J. Y. and Mowbray, S. L. (1994) An evaluation of the use of databases in protein structure refinement. Acta Crystallogr. D50, 237–249.Google Scholar
  9. 9.
    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.Google Scholar
  10. 10.
    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.CrossRefGoogle Scholar
  11. 11.
    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.PubMedCrossRefGoogle Scholar
  12. 12.
    Laskowski, R. A. (2003) Structural quality assurance. In: Structural Bioinformatics, (Bourne, P. E. and Weissig, H., eds.), Wiley-Liss, Hoboken, NJ, pp. 273–303.Google Scholar
  13. 13.
    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.PubMedCrossRefGoogle Scholar
  14. 14.
    Berman, H. M., Westbrook, J., Feng, Z., et al. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235–242.PubMedCrossRefGoogle Scholar
  15. 15.
    Collaborative Computational Project, Nr. 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763.Google Scholar
  16. 16.
    Hooft, R. W. W., Vriend, G., Sander, C. and Abola, E. E. (1996) Errors in protein structures. Nature 381, 272–272.PubMedCrossRefGoogle Scholar
  17. 17.
    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.Google Scholar
  18. 18.
    Kleywegt, G. J. and Jones, T. A. (1996) Efficient rebuilding of protein structures. Acta Crystallogr. D52, 829–832.Google Scholar
  19. 19.
    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.Google Scholar
  20. 20.
    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.Google Scholar
  21. 21.
    Potterton, E., Briggs, P., Turkenburg, M., and Dodson, E. (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr. D59, 1131–1137.Google Scholar
  22. 22.
    Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140–149.Google Scholar
  23. 23.
    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.Google Scholar
  24. 24.
    Kleywegt, G. J. and Read, R. J. (1997) Not your average density. Structure 5, 1557–1569.PubMedCrossRefGoogle Scholar
  25. 25.
    Bhat, T. N. (1988) Calculation of an OMIT map. J. Appl. Crystallogr. 21, 279–281.CrossRefGoogle Scholar
  26. 26.
    Hodel, A., Kim, S. H., and Brünger, A. T. (1992) Model bias in macromolecular crystal structures. Acta Crystallogr. A48, 851–858.Google Scholar
  27. 27.
    Vellieux, F. M. D. and Dijkstra, B. W. (1997) Computation of Bhat’s OMIT map with different coefficients. J. Appl. Crystallogr. 30, 396–399.CrossRefGoogle Scholar
  28. 28.
    Vriend, G. and Sander, C. (1993) Quality control of protein models: directional atomic contact analysis. J. Appl. Crystallogr. 26, 47–60.CrossRefGoogle Scholar
  29. 29.
    Hooft, R. W. W., Sander, C., and Vriend, G. (1996) Verification of protein structures: side-chain planarity. J. Appl. Crystallogr. 29, 714–716.CrossRefGoogle Scholar
  30. 30.
    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.Google Scholar
  31. 31.
    Kleywegt, G. J. and Jones, T. A. (1998) Databases in protein crystallography. Acta Crystallogr. D54, 1119–1131.Google Scholar
  32. 32.
    Jones, T. A. and Kjeldgaard, M. (1997) Electron density map interpretation. Methods Enzymol. 277, 173–208.PubMedCrossRefGoogle Scholar
  33. 33.
    Kleywegt, G. J. and Jones, T. A. (1997) Model-building and refinement practice. Methods Enzymol. 277, 208–230.PubMedCrossRefGoogle Scholar
  34. 34.
    Brünger, A. T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–475.PubMedCrossRefGoogle Scholar
  35. 35.
    Kleywegt, G. J. and Brünger, A. T. (1996) Checking your imagination: applications of the free R value. Structure 4, 897–904.PubMedCrossRefGoogle Scholar
  36. 36.
    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.CrossRefGoogle Scholar
  37. 37.
    Kleywegt, G. J. and Jones, T. A. (1996) Phi/Psi-chology: Ramachandran revisited. Structure 4, 1395–1400.PubMedCrossRefGoogle Scholar
  38. 38.
    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.PubMedCrossRefGoogle Scholar
  39. 39.
    Eisenberg, D., Lüthy, R., and Bowie, J. U. (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277, 396–404.PubMedCrossRefGoogle Scholar
  40. 40.
    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.Google Scholar
  41. 41.
    Kleywegt, G. J. (1996) Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D52, 842–857.Google Scholar
  42. 42.
    Kleywegt, G. J. (1999) Experimental assessment of differences between related protein crystal structures. Acta Crystallogr. D55, 1878–1884.Google Scholar
  43. 43.
    Engh, R. A. and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A47, 392–400.Google Scholar
  44. 44.
    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.Google Scholar
  45. 45.
    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.Google Scholar
  46. 46.
    Jones, T. A., Kleywegt, G. J. and Brünger, A. T. (1996) Storing diffraction data. Nature 381, 18–19.CrossRefGoogle Scholar
  47. 47.
    Brünger, A. T., Kuriyan, J., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics. Science 235, 458–460.PubMedCrossRefGoogle Scholar
  48. 48.
    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.Google Scholar
  49. 49.
    Tronrud, D. E. (1997) The TNT refinement package. Methods Enzymol. 277, 306–319.PubMedCrossRefGoogle Scholar
  50. 50.
    McRee, D. E. (1999) XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165.PubMedCrossRefGoogle Scholar
  51. 51.
    Sheldrick, G. M. and Schneider, T. R. (1997) SHELXL: high-resolution refinement. Methods Enzymol. 277, 319–344.PubMedCrossRefGoogle Scholar
  52. 52.
    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.Google Scholar
  53. 53.
    Colovos, C. and Yeates, T. O. (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Prot. Sci. 2, 1511–1519.CrossRefGoogle Scholar
  54. 54.
    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.Google Scholar
  55. 55.
    Das, U., Chen, S., Fuxreiter, M., et al. (2001) Checking nucleic acid crystal structures. Acta Crystallogr. D57, 813–828.Google Scholar
  56. 56.
    Jones, T. A. (1978) A graphics model building and refinement system for macromolecules. J. Appl. Crystallogr. 11, 268–272.CrossRefGoogle Scholar
  57. 57.
    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.Google Scholar
  58. 58.
    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.Google Scholar
  59. 59.
    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.Google Scholar
  60. 60.
    Jones, T. A. and Liljas, L. (1984) Crystallographic refinement of macromolecules having non-crystallographic symmetry. Acta Crystallogr. A40, 50–57.Google Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Gerard J. Kleywegt
    • 1
  1. 1.Department of Cell and Molecular BiologyUppsala University, Biomedical CenterUppsalaSweden

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