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

Pavel Afonine 1, 2, * Bruno Klaholz 3 Nigel Moriarty 1 Billy Poon 1 Oleg Sobolev 1 Thomas Terwilliger 4 Paul Adams 1, 5 Alexandre Urzhumtsev 3, 6
* Corresponding author
1 Molecular Biophysics and Integrated Bioimaging Division [Berkeley, CA, USA]
2 International Centre for Quantum and Molecular Structures - Department of Physics [Shanghai, China]
3 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
4 LANL - Los Alamos National Laboratory
5 Department of Bioengineering [Berkeley]
6 FST - Faculté des Sciences et Technologies [Université de Lorraine]
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.
Keywords : atomic models cryo-EM data quality model quality resolution validation
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https://www.hal.inserm.fr/inserm-02409756
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Pavel Afonine, Bruno Klaholz, Nigel Moriarty, Billy Poon, Oleg Sobolev, et al.. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta crystallographica. Section D, Structural biology, International Union of Crystallography, 2018, 74 (9), pp.814-840. ⟨10.1107/S2059798318009324⟩. ⟨inserm-02409756⟩

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