Table 21.2.3.3

Wodak, S. J.; Vagin, A. A.; Richelle, J.; Das, U.; Pontius, J.; Berman, H. M.

doi:10.1107/97809553602060000708

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

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International Tables for Crystallography (2006). Vol. F. ch. 21.2, p. 512 | 1 | 2 |

Table 21.2.3.3

S. J. Wodak,^a ^* A. A. Vagin,^b J. Richelle,^b U. Das,^b J. Pontius^b and H. M. Berman^c

^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
Correspondence e-mail: shosh@ucmb.ulb.ac.be

Table 21.2.3.3 | top | pdf |
Parameters computed by SFCHECK to assess the quality of the model in specific regions

The first column lists the parameter, the second column gives the formula or definition of the parameter and the third column contains a short description of the meaning of the parameters when warranted.

Parameter	Formula/definition	Meaning
Shift	$[(1/N\sigma)\textstyle\sum\limits_{i}^{N}\displaystyle \Delta_{i},\hbox{ with } \Delta_{i} = (\hbox{gradient}_{i}/\hbox{curvature}_{i})]$ ^†	Normalized average atomic displacement computed over a group of atoms or residue; reflects the tendency of the group of atoms to move from their current position
Density correlation	$[\displaystyle{\textstyle\sum\displaystyle \rho_{\rm calc}(x_{i})[2\rho_{\rm obs}(x_{i}) - \rho_{\rm calc}(x_{i})] \over \left(\left[\textstyle\sum\displaystyle \rho_{\rm calc}^{2} (x_{i})\right]\left\{\textstyle\sum\displaystyle \left[2\rho_{\rm obs}(x_{i}) - \rho_{\rm calc}(x_{i})\right]^{2}\right\}\right)^{1/2}}]$ ^‡	Electron density correlation coefficient computed over a group of atoms or residue; reflects the local agreement of the model with the electron density
Density index	$[\left[\textstyle\prod\displaystyle \rho(x_{i})\right]^{1/N}/\langle \rho \rangle_{\rm all \ atoms}]$ ^§	Reflects the level of the electron density for a group of atoms; is a local measure of the density level
Connect		Same as Density index, but considering only backbone atoms.^¶

^†Gradient _i is the gradient of the $[F_{\rm obs} - F_{\rm calc}]$ 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 $[\Delta_{i}]$ values computed in the structure.
^‡ $[\rho_{\rm calc}(x_{i})]$ and $[\rho_{\rm obs}(x_{i})]$ 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)

.
^§ $[[\prod{\rho (x_{i})}]^{1/N}]$ is the geometric mean of the $[2F_{\rm obs} - F_{\rm calc}]$ electron density of the atom subset considered and $[\langle \rho \rangle_{\rm all \ atoms}]$ 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 $[\rho(x_i)/\langle \rho \rangle_{\rm all \ atoms}]$ .
^¶Backbone atoms are N, C, C^α for proteins and P, O5′, C5′, C3′, O3′ for nucleic acids.