The productivity of single-particle cryo-EM as a structure determination method has rapidly increased as many novel biological structures are being elucidated. The ultimate result of the cryo-EM experiment is an atomic model that should faithfully represent the computed image reconstruction. Although the principal approach of atomic model building and refinement from maps resembles that of the X-ray crystallographic methods, there are important differences due to the unique properties resulting from the 3D image reconstructions. In this review, we discuss the practiced work-flow from the cryo-EM image reconstruction to the atomic model. We give an overview of (i) resolution determination methods in cryo-EM including local and directional resolution variation, (ii) cryo-EM map contrast optimization including complementary map types that can help in identifying ambiguous density features, (iii) atomic model building and (iv) refinement in various resolution regimes including (v) their validation and (vi) discuss differences between X-ray and cryo-EM maps. Based on the methods originally developed for X-ray crystallography, the path from 3D image reconstruction to atomic coordinates has become an integral and important part of the cryo-EM structure determination work-flow that routinely delivers atomic models.

随着许多新型生物结构的阐明，单粒子冷冻电镜作为一种结构测定方法的生产率迅速提高。冷冻电镜实验的最终结果是一个原子模型，应该忠实地代表计算出的图像重建。尽管从地图构建和细化原子模型的主要方法类似于 X 射线晶体学方法，但由于 3D 图像重建产生的独特属性，存在重要差异。在这篇综述中，我们讨论了从冷冻电镜图像重建到原子模型的实践工作流程。我们概述了 (i) 冷冻电镜中的分辨率确定方法，包括局部和方向分辨率变化，(ii) 冷冻电镜图对比度优化，包括有助于识别模糊密度特征的互补图类型，(iii) 原子模型构建和 (iv) 各种分辨率机制的改进，包括 (v) 验证和 (vi) 讨论两者之间的差异X 射线和冷冻电镜图。基于最初为 X 射线晶体学开发的方法，从 3D 图像重建到原子坐标的路径已成为常规提供原子模型的冷冻电镜结构确定工作流程中不可或缺的重要组成部分。