ArticleJournal of structural biology2022
How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM.
Article in Journal of structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 10 citations in OpenAlex.
- WebCalEM: a browser-based tool for routine and accurate pixel-size calibration in cryo-EM.Acta crystallographica. Section F, Structural biology communications · 2026Article
- Structural basis for HIV-1 Rev recognition by the histone chaperone human Nap1.The Journal of biological chemistry · 2026Article
- WebCalEM: a browser-based tool for routine and accurate pixel size calibration in cryo-EM.bioRxiv : the preprint server for biology · 2026Article
- Cryo-EM meets crystallography: A model-independent view of the heteronuclear MnProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels.The Journal of biological chemistry · 2024Article
- Exploiting the full potential of cryo-EM maps.BBA advances · 2024Article
- Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism.Computational and structural biotechnology journal · 2023Article
- Simulation-predicted and -explained inheritance model of pathogenicity confirmed by transgenic mice models.Computational and structural biotechnology journal · 2023Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20-30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.