Electronic Reprint Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality
Electronic Reprint Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality
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T. Terwilliger;P. D. Adams;R. Read;A. Mccoy;N. Moriarty;R. Grosse-Kunstleve;P. Afonine;P. Zwart-P.-Zwa
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作者：
T. Terwilliger;P. D. Adams;R. Read;A. Mccoy;N. Moriarty;R. Grosse-Kunstleve;P. Afonine;P. Zwart-P.-Zwa
允许在任何媒介上不受限制地使用、分发和复制，只要引用了原始作者和来源。生物结晶学学报D部分：生物结晶学欢迎提交涉及结构生物学各个方面的论文，特别强调生物大分子的结构和测定它们的方法。特别鼓励关于新蛋白质结构的报告，以及结构-功能论文，这些论文可能包括晶体结合研究，或对突变体或已知蛋白质结构的其他修饰形式的结构分析。关键的标准是，这些论文应该提出对生物、化学或结构的新见解。关于结晶学方法的论文应该面向生物结晶学，并可能包括结构测定或分析的任何方面的新方法。对实验图谱质量的估计在大分子结构确定的许多阶段都很重要。地图质量在这里被定义为地图和使用来自最终细化模型的相位获得的相应地图之间的相关性。在这里，使用一组1359张地图来检验10种不同的实验地图质量，这些地图是通过重新分析246个已解算的MAD、SAD和MIR数据集而计算出来的。提出了一种简单的贝叶斯方法，从一个或多个测量来估计地图质量。研究发现，基于电子密度图中密度值的偏斜度的贝叶斯估计器是所考察的10个单独的图质量贝叶斯估计器中最准确的，估计图质量与实际图质量之间的相关性为0.90。电子密度的偏斜度与R.M.S.的局域关联相结合。密度在评价地图质量方面有进一步的改进，总体相关系数为0.92。PHENIX AutoSol向导基于SAD、MAD、SIR或MIR数据集的任意组合执行自动化结构解决方案。该向导基于PHENIX包中的工具，并使用此处描述的地图质量的贝叶斯估计，在试验阶段后选择最高质量的解决方案。
permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure–function papers that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such papers should present new insights into biology, chemistry or structure. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. It was found that a Bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skewness of electron density with the local correlation of r.m.s. density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol wizard carries out automated structure solution based on any combination of SAD, MAD, SIR or MIR data sets. The wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest quality solutions after experimental phasing.