Pintilie Grigore, Shao Chenghua, Wang Zhe, Hudson Brian P, Flatt Justin W, Schmid Michael F, Morris Kyle, Burley Stephen K, Chiu Wah
Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
bioRxiv. 2025 Jan 15:2025.01.14.633006. doi: 10.1101/2025.01.14.633006.
Atomic coordinate models are important in the interpretation of 3D maps produced with cryoEM and sub-tomogram averaging in cryoET, or more generically, 3D electron microscopy (3DEM). In addition to visual inspection of such maps and models, quantitative metrics convey the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, , was shown to correlate well with the reported resolution of the map for well-fitted models. Here we present new statistical analyses of based on its application to 10,000 maps and models archived in EMDB and PDB. Further we introduce two new metrics based on : and to compare a map and model to all entries in the EMDB and those with similar resolution respectively. We also explore through illustrative examples of proteins, nucleic acids, and small molecules how can indicate whether the atomic coordinates are well-fitted to 3DEM maps and whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage, and/or conformational heterogeneity. Lastly, we show examples of how can effectively be converted to atomic . These analyses provide a basis for how can be interpreted effectively to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.
原子坐标模型在解释通过冷冻电镜（cryoEM）和冷冻电子断层扫描（cryoET）中的亚断层平均法生成的三维图谱时非常重要，或者更一般地说，在解释三维电子显微镜（3DEM）图谱时也很重要。除了对这些图谱和模型进行目视检查外，定量指标还能传达原子坐标的可靠性，特别是模型在实验确定的3DEM图谱中的支持程度。最近引入的一个指标 ，对于拟合良好的模型，已被证明与报道的图谱分辨率有很好的相关性。在这里，我们基于其在EMDB和PDB中存档的10000个图谱和模型上的应用，对 进行了新的统计分析。此外，我们基于 引入了两个新指标： 和 ，分别用于将一个图谱和模型与EMDB中的所有条目以及分辨率相似的条目进行比较。我们还通过蛋白质、核酸和小分子的示例，探讨了 如何能够表明原子坐标是否与3DEM图谱拟合良好，以及由于分子柔性、辐射损伤和/或构象异质性等因素，图谱的某些部分是否可能分辨率较差。最后，我们展示了 如何有效地转换为原子 的示例。这些分析为在发表和存档之前如何有效地解释 以评估3DEM图谱和原子坐标模型提供了基础。
