On the accuracy of unit-cell parameters in protein crystallography.

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 Epub Date: 2015-10-31 DOI:10.1107/S1399004715015503

Zbigniew Dauter, Alexander Wlodawer

引用次数: 0

Abstract

The availability in the Protein Data Bank (PDB) of a number of structures that are presented in space group P1 but in reality possess higher symmetry allowed the accuracy and precision of the unit-cell parameters of the crystals of macromolecules to be evaluated. In addition, diffraction images from crystals of several proteins, previously collected as part of in-house projects, were processed independently with three popular software packages. An analysis of the results, augmented by published serial crystallography data, suggests that the apparent precision of the presentation of unit-cell parameters in the PDB to three decimal points is not justified, since these parameters are subject to errors of not less than 0.2%. It was also noticed that processing data including full crystallographic symmetry does not lead to deterioration of the refinement parameters; thus, it is not beneficial to treat the crystals as belonging to space group P1 when higher symmetry can be seen.

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论蛋白质晶体学中单位晶胞参数的准确性。

蛋白质数据库（PDB）中有许多结构以空间群 P1 表示，但实际上具有更高的对称性，因此可以对大分子晶体的单位晶胞参数的准确性和精确性进行评估。此外，之前作为内部项目的一部分而收集的几种蛋白质晶体的衍射图像，也用三种流行的软件包进行了独立处理。根据已公布的序列晶体学数据对结果进行的分析表明，将 PDB 中的单胞参数精确到小数点后三位的做法并不合理，因为这些参数的误差不小于 0.2%。我们还注意到，处理包含完整晶体学对称性的数据并不会导致细化参数的恶化；因此，当可以看到更高的对称性时，将晶体视为属于 P1 空间群是没有益处的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Acta Crystallographica Section D: Biological Crystallography 生物-晶体学

自引率

13.60%

发文量

审稿时长

3 months

期刊介绍： Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.