International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 18.4, p. 401   | 1 | 2 |

Section 18.4.6. Quality assessment of the model

Z. Dauter,a* G. N. Murshudovb and K. S. Wilsonc

aNational Cancer Institute, Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973, USA,bStructural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England, and CLRC, Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, England, and cStructural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
Correspondence e-mail:  dauter@bnl.gov

18.4.6. Quality assessment of the model

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The refinement of proteins at resolution lower than atomic depends upon the use of restraints on the geometry and ADPs. Most target libraries for refinement and validation of structures (e.g. Engh & Huber, 1991[link]) are derived from either the Cambridge Structural Database (Allen et al., 1979[link]) or from protein structures in the Protein Data Bank (PDB; Bernstein et al., 1977[link]). The availability of atomic resolution structures provides more objective data for the construction of target libraries. Stereochemical parameters, such as conformational angles ϕ, ψ, should ideally not be restrained, as they allow independent validation of the model. Analysis of eight structures determined at atomic resolution (EU 3-D Validation Network, 1998[link]) indicates that they follow the expected rules of chemistry more closely than those of lower-resolution analyses in the PDB, confirming that atomic resolution indeed provides more precise coordinates.

References

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
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
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. E., Brice, M. D., Rogers, J. K., 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
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst. A47, 392–400.Google Scholar








































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