Non-uniformity of projection distributions attenuates resolution in Cryo-EM

Prog Biophys Mol Biol. 2020 Jan:150:160-183. doi: 10.1016/j.pbiomolbio.2019.09.002. Epub 2019 Sep 13.


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.

Keywords: Anisotropy; Fourier shell correlation; Preferred orientation; Single particle analysis.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Anisotropy
  • Apoferritins / chemistry*
  • Computer Simulation
  • Cryoelectron Microscopy / instrumentation*
  • Cryoelectron Microscopy / methods*
  • Hemagglutinin Glycoproteins, Influenza Virus / chemistry*
  • Humans
  • Imaging, Three-Dimensional
  • Models, Molecular
  • Molecular Imaging
  • Surface Properties
  • Water


  • Hemagglutinin Glycoproteins, Influenza Virus
  • Water
  • Apoferritins