New tools for the analysis and validation of cryo-EM maps and atomic models.

Pavel V Afonine,Thomas C Terwilliger,Bruno P Klaholz,Alexandre Urzhumtsev,Billy K Poon,Paul D Adams,Oleg V Sobolev,Nigel W Moriarty

doi:10.1107/s2059798318009324

Abstract

Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.

Highlights

While crystallography is still the predominant method for obtaining the three-dimensional atomic structures of macromolecules, the number of near-atomic resolution structures from electron cryomicroscopy is growing exponentially (Fig. 1; Orlov et al, 2017)
Recent advances in the field of electron cryomicroscopy have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods designed for cryo-EM validation are required
This section summarizes the results of the application of the above-described validation tools to models and maps extracted from the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB)

Summary

Introduction

While crystallography is still the predominant method for obtaining the three-dimensional atomic structures of macromolecules, the number of near-atomic resolution structures from electron cryomicroscopy (cryo-EM) is growing exponentially (Fig. 1; Orlov et al, 2017). Crystallographic structure determination is a multi-step process that includes sample preparation, obtaining a crystal of the sample, measuring experimental data from that crystal, solving the phase problem and building an atomic model, followed by model refinement and validation (Rupp, 2010). The collection and processing of experimental data is significantly different in structure determination using cryo-EM because there is no phase problem to solve (Frank, 2006). It has been widely accepted that model validation (Chen et al, 2010) is critical in assessing the correctness of a model from chemical, physical and crystallographic viewpoints, which in turn helps to ensure that the result, the atomic model of a

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Conclusion