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. 21.3, pp. 524-525   | 1 | 2 |

Section 21.3.5.2. Survey of old and revised structures

O. Dym,a D. Eisenbergb* and T. O. Yeatesc

aUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, UCLA, Box 951570, Los Angeles, CA 90095-1570, USA, bUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry & Biochemistry, Molecular Biology Institute and Department of Biological Chemistry, UCLA, Los Angeles, CA 90095-1570, USA, and  cUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry & Biochemistry and Molecular Biology Institute, UCLA, Los Angeles, CA 90095-1569, USA
Correspondence e-mail:  david@mbi.ucla.edu

21.3.5.2. Survey of old and revised structures

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The past two decades have seen a surge of development in the experimental techniques of crystal structure determination. As a consequence, many structures originally solved at low resolution were later determined at higher resolution, often starting with improved phases. The archive of obsolete PDB entries maintained by the San Diego Supercomputer group (http://pdbobs.sdsc.edu ) served as a benchmark for evaluating the ERRAT program. For testing, 17 pairs of protein models were selected. Each pair comprised an obsolete entry and the revised model that replaced it. Using ERRAT, the overall quality of each model was expressed as a single number according to the fraction of the structure falling below the 95% confidence limit for rejection. The overall scores are significantly better for the revised structures, most of which were analysed at improved resolution (Fig. 21.3.5.5a[link]). This result further demonstrates the utility of ERRAT for monitoring the model-building process. Furthermore, a strong correlation is found between the percentage of residues within the 95% confidence limit given by ERRAT and the percentage of residues in the most favoured regions of the Ramachandran plot of PROCHECK (Fig. 21.3.5.5b[link]). In general, the problematic regions detected by the two programs agree with each other.

[Figure 21.3.5.5]

Figure 21.3.5.5 | top | pdf |

Evaluation of old and revised models in a database survey by ERRAT. (a) Percentage of residues within the 95% confidence limit given by ERRAT as a function of the resolution to which the structure was determined. Each arrow represents an obsolete structure (arrow tail) and the revised structure that replaced it (arrow head). The revised structures (typically analysed at finer resolution) show markedly improved ERRAT scores. (b) Correlation between the percentage of a structure within the 95% confidence limit according to ERRAT, and the percentage of residues in the most favoured regions of a Ramachandran diagram according to PROCHECK.








































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