Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Department of Biochemistry, Duke University, Durham, NC 27710, USA.
Acta Crystallogr D Struct Biol. 2021 Jan 1;77(Pt 1):48-61. doi: 10.1107/S2059798320015879.
The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.
近年来，随着众多技术和方法学的发展，电子晶体学显微镜（cryo-EM）领域发展迅速。这导致使用该方法确定的原子结构数量有所增加。最近，在 Phenix 软件包中开发了一些用于分析 cryo-EM 数据和模型的工具，例如 phenix.real_space_refine，用于根据实空间图对原子模型进行精修。此外，还为低分辨率 cryo-EM 模型开发了新的验证指标。为了了解已存储的 cryo-EM 结构的质量以及如何改进它们，可以使用当前版本的 Phenix 工具自动重新精修在蛋白质数据库（PDB）中分辨率优于 5 Å 的 map 的模型。结果可在公共访问网页（https://cci.lbl.gov/ceres）上获得。描述了为改进 wwPDB 中存储的模型而实施的 Cryo-EM Re-refinement System (CERES) 以及重新精修的结果。基于这些结果，提出了一个“cryo-EM 表 1”的内容，该表以类似于晶体学中“表 1”的方式总结实验细节和验证指标。在每个结构存储时，都应使用稳健的指标来评估 cryo-EM 模型和数据，并在科学出版物中进行报告。
