Table 21.2.3.1

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. 511 | 1 | 2 |

Table 21.2.3.1

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 21.2.3.1 | top | pdf |
Parameters computed for the analysis of the structure-factor data

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
Completeness (%)	Percentage of the expected number of reflections for the given crystal space group and resolution
B_overall (Patterson)	$[8\pi^{2} \sigma_{\rm Patt}/(2)^{1/2}]$ ^†	Overall B factor
R_stand(F)	$[\langle \sigma (F)\rangle/\langle F \rangle]$ ^‡	Uncertainty of the structure-factor amplitudes
Optical resolution	$[(\sigma_{\rm Patt}^{2} + \sigma_{\rm sph}^{2})^{1/2}]$ ^† ^§	Expected minimum distance between two resolved atomic peaks
Expected optical resolution	Optical resolution computed considering all reflections
$[\hbox{CC}_{F}]$	$[\displaystyle{\langle F_{\rm obs} F_{\rm calc}\rangle - \langle F_{\rm obs}\rangle\langle F_{\rm calc}\rangle \over \left[(\langle F_{\rm obs}^{2} \rangle - \langle F_{\rm obs}\rangle^{2}) (\langle F_{\rm calc}^{2}\rangle - \langle F_{\rm calc}\rangle^{2})\right]^{1/2}}]$	Correlation coefficient between the observed and calculated structure-factor amplitudes
S	$[\left\{{\textstyle\sum\displaystyle (F_{\rm obs} f_{\rm cutoff})^{2} \over \textstyle\sum\displaystyle \left[F_{\rm calc} \exp (- B_{\rm diff}^{\rm overall} s^{2}) f_{\rm cutoff}\right]^{2}}\right\}^{1/2}]$ ^¶	Factor applied to scale $[F_{\rm calc}]$ to $[F_{\rm obs}]$
$[f_{\rm cutoff}]$	$[1 - \exp (- B_{\rm off} s^{2})]$ ^††	Function applied to obtain a smooth cutoff for low-resolution data

^† $[\sigma_{\rm Patt}]$ is the standard deviation of the Gaussian fitted to the Patterson origin peak.
^‡F is the structure-factor amplitude, and $[\sigma({F})]$ is the structure-factor standard deviation. The brackets denote averages.
^§ $[\sigma _{\rm sph}]$ is the standard deviation of the spherical interference function, which is the Fourier transform of a sphere of radius $[1/d_{\min}]$ , with $[d_{\rm min}]$ being the minimum d spacing.
^¶ $[B_{\rm diff}^{\rm overall} = B_{\rm obs}^{\rm overall} - B_{\rm calc}^{\rm overall}]$ is added to the calculated overall B factor, $[B_{\rm overall}]$ , so as to make the width of the calculated Patterson origin peak equal to the observed one; s is the magnitude of reciprocal-lattice vector.
^†† $[B_{\rm off} = 4 d_{\rm max}^{2}]$ , where s and $[d_{\rm max}]$ , respectively, are the magnitude of the reciprocal-lattice vector and the maximum d spacing.