Crystallographic model quality at a glance.
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.
Urzhumtseva
Ludmila
L
Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, Strasbourg, France.
Afonine
Pavel V
PV
Adams
Paul D
PD
Urzhumtsev
Alexandre
A
D000465:Algorithms; D003196:Computer Graphics; D018360:Crystallography, X-Ray / Q000706:statistics & numerical data; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D013237:Stereoisomerism; D054928:Validation Studies as Topic
D046911:Macromolecular Substances