Open Access

IUCrJ, volume 6, issue 1, pages 5-17

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis

Zivanov Jasenko ¹

Nakane Takanori ¹

Scheres Sjors H. W. ¹

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Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England |

Publication type: Journal Article

Publication date: 2019-01-01

International Union of Crystallography (IUCr)

Journal: IUCrJ

Quartile SCImago

Quartile WOS

Impact factor: 3.9

ISSN: 20522525

DOI: 10.1107/S205225251801463X

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PubMed ID: 30713699

General Chemistry

Biochemistry

Condensed Matter Physics

General Materials Science

Abstract

A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.

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	50 100 150 200 250
Springer Nature	Springer Nature, 201, 29.91% Springer Nature 201 publications, 29.91%
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Biophysical Society	Biophysical Society, 1, 0.15% Biophysical Society 1 publication, 0.15%
Walter de Gruyter	Walter de Gruyter, 1, 0.15% Walter de Gruyter 1 publication, 0.15%
IEEE	IEEE, 1, 0.15% IEEE 1 publication, 0.15%
Rockefeller University Press	Rockefeller University Press, 1, 0.15% Rockefeller University Press 1 publication, 0.15%
Cambridge University Press	Cambridge University Press, 1, 0.15% Cambridge University Press 1 publication, 0.15%
American Society for Microbiology	American Society for Microbiology, 1, 0.15% American Society for Microbiology 1 publication, 0.15%
	50 100 150 200 250

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Zivanov J., Nakane T., Scheres S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis // IUCrJ. 2019. Vol. 6. No. 1. pp. 5-17.

GOST all authors (up to 50) Copy

Zivanov J., Nakane T., Scheres S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis // IUCrJ. 2019. Vol. 6. No. 1. pp. 5-17.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1107/S205225251801463X

UR - https://doi.org/10.1107%2FS205225251801463X

TI - A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis

T2 - IUCrJ

AU - Zivanov, Jasenko

AU - Nakane, Takanori

AU - Scheres, Sjors H. W.

PY - 2019

DA - 2019/01/01 00:00:00

PB - International Union of Crystallography (IUCr)

SP - 5-17

IS - 1

VL - 6

PMID - 30713699

SN - 2052-2525

ER -

BibTex |

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BibTex Copy

@article{2019_Zivanov,

author = {Jasenko Zivanov and Takanori Nakane and Sjors H. W. Scheres},

title = {A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis},

journal = {IUCrJ},

year = {2019},

volume = {6},

publisher = {International Union of Crystallography (IUCr)},

month = {jan},

url = {https://doi.org/10.1107%2FS205225251801463X},

number = {1},

pages = {5--17},

doi = {10.1107/S205225251801463X}

}

MLA

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MLA Copy

Zivanov, Jasenko, et al. “A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis.” IUCrJ, vol. 6, no. 1, Jan. 2019, pp. 5-17. https://doi.org/10.1107%2FS205225251801463X.

Found error?

Publisher

International Union of Crystallography (IUCr)

Journal

IUCrJ

Quartile SCImago

Quartile WOS

Impact factor

3.9

ISSN

20522525 (Electronic)