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Showing 1–15 of 15 results
Advanced filters: Author: Pavel V. Afonine Clear advanced filters

  • This Primer offers a practical and rational introduction to macromolecular crystallography, whether to engage directly with or to critically assess results, with a focus on understanding the diffraction data, solving the phase problem, building and refining the atomic model, and interpreting the resulting atomic structure.

    • Pavel V. Afonine
    • Armando Albert
    • Isabel Usón
    Reviews
    Nature Reviews Methods Primers
    Volume: 5, P: 1-25

  • The number of K+ occupied binding sites in the selectivity filter of potassium ion channels is still under debate. Here, the authors collect diffraction data on the K+ selective NaK channel NaK2K at a wavelength of 3.35 Å, close to the K absorption edge, revealing that all four binding sites in the selectivity filter are fully occupied by K+ ions.

    • Patricia S. Langan
    • Venu Gopal Vandavasi
    • Leighton Coates
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-5

  • The EMDataResource Ligand Model Challenge aimed at assessing the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryo-EM maps determined at near-atomic resolution. This analysis presents the results and recommends best practices for assessing cryo-EM structures of liganded macromolecules.

    • Catherine L. Lawson
    • Andriy Kryshtafovych
    • Wah Chiu
    Research
    Nature Methods
    Volume: 21, P: 1340-1348

  • A multi-laboratory study in the form of a community challenge assesses the quality of models that can be produced from cryo-EM maps using different software tools, the reproducibility of models generated by different users and the performance of metrics used for model validation.

    • Catherine L. Lawson
    • Andriy Kryshtafovych
    • Wah Chiu
    ResearchOpen Access
    Nature Methods
    Volume: 18, P: 156-164

  • An analysis of AlphaFold protein structure predictions shows that while in many cases the predictions are highly accurate, there are also many instances where the predicted structures or parts of predicted structures do not agree with experimentally resolved data. Therefore, care must be taken when using these predictions for informing structural hypotheses.

    • Thomas C. Terwilliger
    • Dorothee Liebschner
    • Paul D. Adams
    ResearchOpen Access
    Nature Methods
    Volume: 21, P: 110-116

  • This paper presents an iterative procedure where AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions.

    • Thomas C. Terwilliger
    • Billy K. Poon
    • Paul D. Adams
    ResearchOpen Access
    Nature Methods
    Volume: 19, P: 1376-1382

  • Recent developments in cryo-electron microscopy have enabled structure determination of large protein complexes at almost atomic resolution. Wang et al.combine some of these technologies into an effective workflow, and demonstrate the protocol by solving the atomic structure of an icosahedral RNA virus.

    • Zhao Wang
    • Corey F. Hryc
    • Wah Chiu
    ResearchOpen Access
    Nature Communications
    Volume: 5, P: 1-12

  • A method based on maximum likelihood density modification, adapted from X-ray crystallography, improves cryo-EM maps.

    • Thomas C. Terwilliger
    • Steven J. Ludtke
    • Pavel V. Afonine
    Research
    Nature Methods
    Volume: 17, P: 923-927

  • The ability of constrained mutants of the estrogen receptor ligand-binding domain to dictate different conformations of bound partial agonists indicates that the ability of compounds to stabilize each state determines the degree of agonist activity.

    • John B Bruning
    • Alexander A Parent
    • Kendall W Nettles
    Research
    Nature Chemical Biology
    Volume: 6, P: 837-843

  • Tailed bacteriophages assemble empty precursor capsids known as procapsids that are subsequently filled with viral DNA by a genome-packaging motor. Here the authors present a structure-based analysis that suggests the signal for termination of genome packaging is achieved through a DNA-dependent symmetrization of portal protein.

    • Ravi K. Lokareddy
    • Rajeshwer S. Sankhala
    • Gino Cingolani
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-11

  • The cryo-electron microscopy structure of the ten-subunit human transcription factor IIH, revealing the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected.

    • Basil J. Greber
    • Thi Hoang Duong Nguyen
    • Eva Nogales
    Research
    Nature
    Volume: 549, P: 414-417

  • READ is a new crystallographic approach to visualize conformational ensembles of heterogeneous and dynamic molecules. READ is applied here to structurally characterize the various folding states of client Im7 bound to chaperone Spy.

    • Scott Horowitz
    • Loïc Salmon
    • James C A Bardwell
    Research
    Nature Structural & Molecular Biology
    Volume: 23, P: 691-697