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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?
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Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?

机译：立体化学的限制再现:如何准确细化目标,应该多少蛋白质结构被允许偏离他们吗?

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摘要

The Protein Data Bank and Cambridge Structural Database were analyzed with the aim of verifying whether the restraints that are most commonly used for protein structure refinement are still appropriate 15 years after their introduction. From an analysis of selected main-chain parameters in well ordered fragments of ten highest resolution protein structures, it was concluded that some of the currently used geometrical target values should be adjusted somewhat (the C-N bond and the N-C(alpha)-C angle) or applied with less emphasis (peptide planarity). It was also found that the weighting of stereochemical information in medium-resolution refinements is often overemphasized at the cost of the experimental information in the diffraction data. A correctly set balance will be reflected in root-mean-square deviations from ideal bond lengths in the range 0.015-0.020 A for structures refined to R factors of 0.15-0.20. At ultrahigh resolution, however, the diffraction terms should be allowed to dominate, with even higher acceptable deviations from idealized standards in the well defined fragments of the protein. It is postulated that modern refinement programs should accommodate variable restraint weights that are dependent on the occupancies and B factors of the atoms involved.
机译：蛋白质数据银行和剑桥的结构数据库进行了分析与验证的目的最常见的限制用于蛋白质结构细化仍适当的15年之后他们的介绍。从一个选定的主链的分析参数命令十的碎片最高分辨率的蛋白质结构,它是得出的结论是,目前的一些使用几何目标应调整值有些(碳氮键和c - c(α)角(肽)或应用以更少的重点平面性)。立体化学的信息中分辨率细分通常是过份强调实验的成本在衍射数据的信息。平衡将反映在均方根偏离理想的债券的长度范围内0.015 - -0.020为结构改进R因素0.15 - -0.20。衍射条件应该被允许占据主导地位,甚至更高的可接受的偏差理想化的标准的定义片段的蛋白质。应该适应现代优化程序依赖的变量约束权重入住率和B原子的因素参与。

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