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

By Pavel V. Afonine, Bruno P. Klaholz, Nigel W. Moriarty, Billy K. Poon, O. Sobolev, T. C. Terwilliger, Paul D. Adams, Alexandre Urzhumtsev. 2018

691 citations recorded by the source corpus.

Recent advances in the field of electron cryo-microscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of bio-macromolecules 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 for cryo-EM validation are required. We discuss new computational methods and tools implemented in Phenix, including d99 to estimate resolution, phenix.auto_sharpen to improve maps, and phenix.mtriage to analyze cryo-EM maps. We suggest that cryo-EM half-maps and masks are deposited to facilitate evaluation and validation of cryo-EM derived atomic models and maps. We also present the application of these tools to deposited cryo-EM atomic models and maps.

Subfields: Condensed Matter Physics, Structural Biology, Surfaces, Coatings and Films

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In Condensed Matter Physics

T. Croll

In Structural Biology

In Surfaces, Coatings and Films

Citations in the corpus

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands (2022, positive): “Then the models were refined against the cryo-EM maps using phenix.real_space_refine within phenix and refmac5 within the ccpem software suit (Afonine et al., 2018; Burnley et al., 2017).”
RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli–Pepper aptamer FRET pair (2023, methodology): “Validation of the goodness of fit between model and map were performed using the Phenix validation tool (43,45,46).”
The human coronavirus HCoV-229E S-protein structure and receptor binding (2019, methodology): “The atomic model 575 was refined against a half-map using Phenix.real_space_refine (62) and Rosetta (63).”
Structural insights into the assembly and activation of the IL‐27 signaling complex (2022, methodology): “The initial model of IL-27 was refined into the cryoEM map using ISOLDE (v.1.3; Croll, 2018) (v.1.20.1-4487; Afonine et al , 2018) with secondary structure, reference model, and geometry restraints.”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “All statistics other than EM model– map correlation were gathered from the wwPDB validation reports (Read et al., 2011); the latter were gathered from a previous analysis (Afonine et al., 2018).”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “5, which reports on both model and map quality.(204) Alternatively, it has been shown that integrating the FSC curves across the mid-low resolution range (6–10 Å) produces a score (FSCi) that is slightly more discriminative than real space correlation (CC).”
Cryo-EM targets in CASP13: overview and evaluation of results (2019, methodology): “However, in practice evenmodels built on such well-resolved maps are not void of structural inconsistencies or errors.(23,28) In this section, we analyzewhether CASPmodels, which are built without the knowledge of the cryo-EM density, agree with the density, and compare their goodness-of-fit with th”
The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction (2022, methodology): “Real-space refinement and structure validation [28]”