Reliable cryo-EM resolution estimation with modified Fourier shell correlation

IUCrJ
Pawel A Penczek

Abstract

A modified Fourier shell correlation (mFSC) methodology is introduced that is aimed at addressing two fundamental problems that mar the use of the FSC: the strong influence of mask-induced artifacts on resolution estimation and the lack of assessment of FSC uncertainties stemming from the inability to determine the associated number of degrees of freedom. It is shown that by simply changing the order of the steps in which the FSC is computed, the correlations induced by masking of the input data can be eliminated. In addition, to further reduce artifacts, a smooth Gaussian window function is used to outline the regions of reciprocal space within which the mFSC is computed. Next, it is shown that the number of degrees of freedom (ndf) of the system is approximated well by combining the ndf associated with the Gaussian window in reciprocal space with further reduction of the ndf owing to the use of the mask in real space. It is demonstrated through the application of the mFSC to both single-particle and helical structures that the mFSC yields reliable, mask-induced artifact-free results as a result of the introduced modifications. Since the adverse effect of the mask is eliminated, it also becomes possible to compute robust local...Continue Reading

References

Jan 1, 1987·Ultramicroscopy·M UnserA C Steven
Aug 1, 1982·Journal of Microscopy·W O Saxton, W Baumeister
Jul 25, 2006·Journal of Structural Biology·Guang TangSteven J Ludtke
Aug 26, 2006·Journal of Structural Biology·Michael HohnSteven J Ludtke
Oct 13, 2006·Journal of Structural Biology·Duncan Sousa, Nikolaus Grigorieff
Oct 5, 2010·Methods in Enzymology·Pawel A Penczek
Oct 5, 2010·Methods in Enzymology·Ruben DiazDavid L Stokes
Oct 5, 2010·Methods in Enzymology·Fred J SigworthSjors H W Scheres
Aug 21, 2013·Journal of Structural Biology·Giovanni CardoneAlasdair C Steven
Nov 12, 2013·Nature Methods·Alp KucukelbirHemant D Tagare
Feb 25, 2014·Ultramicroscopy·Pawel A PenczekChristian M T Spahn
Apr 25, 2015·Cell·Yifan ChengThomas Walz
Apr 29, 2015·Archives of Biochemistry and Biophysics·Edward H Egelman
May 11, 2015·Cell·Elmar BehrmannChristian M T Spahn
Mar 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Yuxi LiuTodd O Yeates
Jul 10, 2020·Current Opinion in Structural Biology·J L VilasCos Sorzano

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Datasets Mentioned

BETA
EMPIAR-10028

Methods Mentioned

BETA
electron microscopy

Software Mentioned

py
sxmeridien
SciPy
e2segment3d
SPARX
HELICON
EMAN
FFTW3

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