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Cryo-electron Microscopy

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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...

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Updated: Dec 13, 2025

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

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Structural interpretation of cryo-EM image reconstructions.

Maximilian Beckers¹, Daniel Mann², Carsten Sachse³

¹European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany; Candidate for Joint PhD Degree from EMBL and Heidelberg University, Faculty of Biosciences, Germany; Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany.

Progress in Biophysics and Molecular Biology

|August 1, 2020

Summary

This summary is machine-generated.

Single-particle cryo-electron microscopy (cryo-EM) now routinely generates atomic models from 3D reconstructions. This review details the workflow from image processing to model validation, highlighting differences from X-ray crystallography.

Keywords:

Atomic model Cryo-EM Map interpretation Map variation Molecular modelling Resolution Sharpening

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Area of Science:

Structural Biology
Biophysics

Background:

Single-particle cryo-electron microscopy (cryo-EM) is a rapidly advancing technique for determining biological structures.
The accuracy of the final atomic model is crucial for representing the cryo-EM image reconstruction.

Purpose of the Study:

To review the workflow for building and refining atomic models from cryo-EM data.
To highlight key differences and considerations compared to X-ray crystallography.

Main Methods:

Overview of resolution determination, including local and directional variations.
Discussion of cryo-EM map contrast optimization and complementary map types.
Detailed examination of atomic model building and refinement strategies across different resolution ranges.
Validation methods for cryo-EM derived atomic models.

Main Results:

The process from 3D image reconstruction to atomic coordinates is now a standard part of the cryo-EM workflow.
Atomic models derived from cryo-EM routinely achieve high accuracy.
Understanding differences between cryo-EM and X-ray maps is essential for accurate model interpretation.

Conclusions:

Cryo-EM structure determination workflow, adapted from X-ray crystallography, now routinely yields accurate atomic models.
The review provides a comprehensive guide to navigating the process from cryo-EM data to validated atomic models.