Factors influencing estimates of coordinate error for molecular replacement.
Factors influencing estimates of coordinate error for molecular replacement.
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影响分子替换坐标误差估计的因素。
DOI：
10.1107/s2059798319015730
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Hatti KS
中科院分区：
文献类型：
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作者：
Hatti KS
有效均方根偏差（r.m.s.d.）的良好先验估计模型和目标的原子坐标之间的相互作用优化了分子置换中的信号，从而提高了困难情况下的成功率。以前的研究使用X射线晶体学解决的蛋白质结构作为模型表明，最佳误差估计（结构解决方案后细化）与模型和目标之间的序列同一性，并与模型中的残基数量相关。在这里，这项工作已被扩展到找到额外的模型和目标的参数之间的相关性，从而提高了坐标误差的先验估计。使用图形数据库，分析了一组6030个分子置换计算，这些计算使用的模型已经通过X射线晶体学求解，以考虑大约120个模型和目标参数。通过将序列同一性替换为序列相似性的Gonnet评分，以及通过考虑目标结构的分辨率和模型的MolProbity评分，实现了改进的估计。通过分析12610个额外的分子置换计算，其中该模型由NMR确定，扩展了这种方法。 平均相对标准偏差在一个集合中的模型对之间被发现与估计的r.m.s. d相关。到目标对于通过NMR解决的模型，总体坐标误差估计值大于通过X射线晶体学确定的结构，并且与残基的数量更高度相关。
Good prior estimates of the effective root-mean-square deviation (r.m.s.d.) between the atomic coordinates of the model and the target optimize the signal in molecular replacement, thereby increasing the success rate in difficult cases. Previous studies using protein structures solved by X-ray crystallography as models showed that optimal error estimates (refined after structure solution) were correlated with the sequence identity between the model and target, and with the number of residues in the model. Here, this work has been extended to find additional correlations between parameters of the model and the target and hence improved prior estimates of the coordinate error. Using a graph database, a curated set of 6030 molecular-replacement calculations using models that had been solved by X-ray crystallography was analysed to consider about 120 model and target parameters. Improved estimates were achieved by replacing the sequence identity with the Gonnet score for sequence similarity, as well as by considering the resolution of the target structure and the MolProbity score of the model. This approach was extended by analysing 12 610 additional molecular-replacement calculations where the model was determined by NMR. The median r.m.s.d. between pairs of models in an ensemble was found to be correlated with the estimated r.m.s.d. to the target. For models solved by NMR, the overall coordinate error estimates were larger than for structures determined by X-ray crystallography, and were more highly correlated with the number of residues.