Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive
Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive
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DOI：
10.1016/j.str.2017.01.013
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发表时间：
2017-03-07
期刊：
影响因子：
5.7
通讯作者：
Burley, Stephen K.
中科院分区：
文献类型：
--
作者：
Shao, Chenghua;Yang, Huanwang;Burley, Stephen K.
在全球蛋白质数据库（wwPDB）合作伙伴部署增强验证系统后，进入PDB的晶体结构质量得到了改善。重要的是质量措施的改进，现在突出显示在wwPDB验证报告中。PDB沉积之前和之后引入新的报告系统的比较表明，改进的质量措施有关的成对原子-原子的冲突，侧链扭转角旋转异构体，和本地协议之间的原子坐标结构模型和实验电子密度数据。这些改进在很大程度上与分辨率极限和样品分子量无关。没有观察到相关配体质量的显著改善。主成分分析表明，结构质量可以概括为三个措施（Rfree，realspace R因子Z得分，并结合分子几何质量度量），这反过来又可以减少到一个单一的整体质量度量易于解释的所有PDB档案用户。
Following deployment of an augmented validation system by the Worldwide Protein Data Bank (wwPDB) partnership, the quality of crystal structures entering the PDB has improved. Of significance are improvements in quality measures now prominently displayed in the wwPDB validation report. Comparisons of PDB depositions made before and after introduction of the new reporting system show improvements in quality measures relating to pairwise atom-atom clashes, side-chain torsion angle rotamers, and local agreement between the atomic coordinate structure model and experimental electron density data. These improvements are largely independent of resolution limit and sample molecular weight. No significant improvement in the quality of associated ligands was observed. Principal component analysis revealed that structure quality could be summarized with three measures (Rfree, realspace R factor Z score, and a combined molecular geometry quality metric), which can in turn be reduced to a single overall quality metric readily interpretable by all PDB archive users.