Preserving information and integrity in Cryo-EM: Toward a Fourier-space deposition approach.

Authors

Zbyszek Otwinowski, Yirui Guo, Raquel Bromberg, Dominika Borek

Published in

Journal of structural biology. Pages 108385. Oct 29, 2026. Epub Oct 29, 2026.

Abstract

Current guidelines for depositing cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) data require submission of unfiltered, unmasked, and unsharpened raw half-maps. The Fourier Shell Correlation (FSC) between the half-maps is then used as a proxy for the signal-to-noise ratio (SNR) to estimate the reconstruction's resolution. This policy was introduced to enable independent validation of reported resolutions. Although developed to safeguard data integrity and minimize bias, these guidelines do not account for specific features of modern cryo-EM processing software, in particular weighting schemes that are not retained in half-map depositions and yet in general are necessary to recapitulate resolution estimates. As a result, resolution estimates and other validation statistics based on half-map FSC may be under- or overestimated. Here, we describe the limitations of the current deposition guidelines and propose an alternative: depositing cryo-EM results in Fourier (reciprocal) space together with the mandatory deposition of molecular masks or their descriptors. This approach would address the current limitations, preserve critical information from the reconstruction process, and better support downstream analyses.

PMID:
42956948
Bibliographic data and abstract were imported from PubMed on 30 Oct 2026.

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