Publication Date
1-1-2020
Journal
Progress in Biophysics and Molecular Biology
DOI
10.1016/j.pbiomolbio.2019.09.002
PMID
31525386
PMCID
PMC7054125
PubMedCentral® Posted Date
1-1-2021
PubMedCentral® Full Text Version
Author MSS
Published Open-Access
yes
Keywords
Algorithms, Anisotropy, Apoferritins, Computer Simulation, Cryoelectron Microscopy, Hemagglutinin Glycoproteins, Influenza Virus, Humans, Imaging, Three-Dimensional, Models, Molecular, Molecular Imaging, Surface Properties, Water, Fourier Shell Correlation, single particle analysis, preferred orientation, anisotropy
Abstract
Virtually all single-particle cryo-EM experiments currently suffer from specimen adherence to the air-water interface, leading to a non-uniform distribution in the set of projection views. Whereas it is well accepted that uniform projection distributions can lead to high-resolution reconstructions, non-uniform (anisotropic) distributions can negatively affect map quality, elongate structural features, and in some cases, prohibit interpretation altogether. Although some consequences of non-uniform sampling have been described qualitatively, we know little about how sampling quantitatively affects resolution in cryo-EM. Here, we show how inhomogeneity in any projection distribution scheme attenuates the global Fourier Shell Correlation (FSC) in relation to the number of particles and a single geometrical parameter, which we term the sampling compensation factor (SCF). The reciprocal of the SCF is defined as the average over Fourier shells of the reciprocal of the per-particle sampling and normalized to unity for uniform distributions. The SCF therefore ranges from one to zero, with values close to the latter implying large regions of poorly sampled or completely missing data in Fourier space. Using two synthetic test cases, influenza hemagglutinin and human apoferritin, we demonstrate how any amount of sampling inhomogeneity always attenuates the FSC compared to a uniform distribution. We advocate quantitative evaluation of the SCF criterion to approximate the effect of non-uniform sampling on resolution within experimental single-particle cryo-EM reconstructions.