Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, UK.
Faraday Discuss. 2022 Nov 8;240(0):196-209. doi: 10.1039/d2fd00103a.
Cryogenic electron microscopy (cryo-EM) has recently been established as a powerful technique for solving macromolecular structures. Although the best resolutions achievable are improving, a significant majority of data are still resolved at resolutions worse than 3 Å, where it is non-trivial to build or fit atomic models. The map reconstructions and atomic models derived from the maps are also prone to errors accumulated through the different stages of data processing. Here, we highlight the need to evaluate both model geometry and fit to data at different resolutions. Assessment of cryo-EM structures from SARS-CoV-2 highlights a bias towards optimising the model geometry to agree with the most common conformations, compared to the agreement with data. We present the CoVal web service which provides multiple validation metrics to reflect the quality of atomic models derived from cryo-EM data of structures from SARS-CoV-2. We demonstrate that further refinement can lead to improvement of the agreement with data without the loss of geometric quality. We also discuss the recent CCP-EM developments aimed at addressing some of the current shortcomings.
低温电子显微镜（cryo-EM）最近已被确立为解决大分子结构的强大技术。尽管可达到的最佳分辨率在不断提高，但仍有很大一部分数据的分辨率低于 3 Å，在这种分辨率下，构建或拟合原子模型并非易事。从映射中得出的映射重建和原子模型也容易受到通过数据处理的不同阶段积累的错误的影响。在这里，我们强调需要在不同的分辨率下评估模型几何形状和拟合数据。来自 SARS-CoV-2 的 cryo-EM 结构的评估突出了一种偏向于优化模型几何形状以与最常见构象一致的趋势，而不是与数据一致。我们展示了 CoVal 网络服务，该服务提供了多种验证指标，以反映来自 SARS-CoV-2 结构的 cryo-EM 数据导出的原子模型的质量。我们证明，进一步细化可以提高与数据的一致性，而不会损失几何质量。我们还讨论了最近的 CCP-EM 开发，旨在解决当前的一些缺点。
