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, p. 511
Section 21.2.3.1.1.4. Local agreement between the model and the experimental data
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 |
In addition to the global structure quality measures, SFCHECK also determines the quality of the model in specific regions. Several quality estimators can be calculated for each residue in the macromolecule and, whenever appropriate, for solvent molecules and groups of atoms in ligand molecules. These estimators are the normalized atomic displacement (Shift), the correlation coefficient between the calculated and observed electron densities (Density correlation), the local electron-density level (Density index), the average B factor (B-factor) and the connectivity index (Connect), which measures the local electron-density level along the molecular backbone. These quantities are computed for individual atoms and averaged over those composing each residue or group of atoms [see Table 21.2.3.3 and Vaguine et al. (1999) for details].
†Gradient i is the gradient of the map with respect to the atomic coordinates, curvature i is the curvature of the model map computed at the atomic centre (see Agarwal, 1978), N is the number of atoms in the group considered and σ is the standard deviation of the values computed in the structure.
‡ and are, respectively, the electron density computed from calculated and observed structure-factor amplitudes at the atomic centre. The summation is performed over all the atoms in the group considered. For polymer residues, D_corr is computed separately for backbone and side-chain atoms. For the calculation of the electron density at the atomic centre, see Vaguine et al. (1999). § is the geometric mean of the electron density of the atom subset considered and is the average electron density of the atoms in the structure. For water molecules or ions which are represented by a unique atom, the above expression reduces to the ratio . ¶Backbone atoms are N, C, Cα for proteins and P, O5′, C5′, C3′, O3′ for nucleic acids. |
References
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