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, 65 (Pt 3), 297-300

Crystallographic Model Quality at a Glance

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Crystallographic Model Quality at a Glance

Ludmila Urzhumtseva et al. Acta Crystallogr D Biol Crystallogr.

Abstract

A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from ;ideal values' is shown graphically as a point on a ;ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in ;red zones' indicate parameters which lie outside typical values.

Figures

Figure 1
Figure 1
Examples of the polygon presentation of model characteristics. The values bndav, angav, dihav and plnav are the mean deviations from the standard values for bonds, angles, dihedral angles and plane groups, respectively; bndmx, angmx, dihmx and plnmx are their maximal values. adpav and adpmx are the mean and maximal values of the atomic displacement parameters or their isotropic equivalents. Axes are coloured accordingly to the frequency of the model characteristics for the selected set of PDB models with a particular resolution (given in the upper right corner). The values of the given frequency (for example, green for a frequency between 1 and 2) show how much higher or lower it is than the frequency for the uniform distribution. See the text for details and comments.

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