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Crystallographic model quality at a glance.

Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A - Acta Crystallogr. D Biol. Crystallogr. (2009)

Bottom Line: 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.Polygon vertices in ;red zones' indicate parameters which lie outside typical values.

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Affiliation: Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, Strasbourg, France.

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.

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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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fig1: 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.

Mentions: We used phenix.model_vs_data to homogenously compute model and data statistics such as R factors or stereochemical deviations (PHENIX uses the CCP4 Monomer Library; Vagin et al., 2004 ▶). The original values of the R factors from the headers of the PDB files can be displayed at additional axes of the polygon (see, for example, the axes rpdb and rfpdb in Figs. 1 ▶ e and 1 ▶ f). The models with a large difference between reported and calculated R factors can be filtered out by request.


Crystallographic model quality at a glance.

Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A - Acta Crystallogr. D Biol. Crystallogr. (2009)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651759&req=5

fig1: 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.
Mentions: We used phenix.model_vs_data to homogenously compute model and data statistics such as R factors or stereochemical deviations (PHENIX uses the CCP4 Monomer Library; Vagin et al., 2004 ▶). The original values of the R factors from the headers of the PDB files can be displayed at additional axes of the polygon (see, for example, the axes rpdb and rfpdb in Figs. 1 ▶ e and 1 ▶ f). The models with a large difference between reported and calculated R factors can be filtered out by request.

Bottom Line: 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.Polygon vertices in ;red zones' indicate parameters which lie outside typical values.

View Article: PubMed Central - HTML - PubMed

Affiliation: Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, Strasbourg, France.

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.

Show MeSH
Related in: MedlinePlus