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Related Concept Videos

Cryo-electron Microscopy01:28

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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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
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Updated: Apr 18, 2026

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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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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Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions.

Alan Brown1, Fei Long1, Robert A Nicholls1

  • 1MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England.

Acta Crystallographica. Section D, Biological Crystallography
|January 24, 2015
PubMed
Summary

New computational tools enhance the interpretation of cryo-electron microscopy (cryo-EM) density maps. These advancements facilitate building accurate all-atom models for protein and nucleic acid structures.

Keywords:
LIBGelectron cryo-microscopy reconstructionsmodel buildingrefinement

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Single-particle cryo-electron microscopy (cryo-EM) is achieving resolutions near 3 Å.
  • Interpreting cryo-EM density maps to build accurate atomic models remains a challenge.

Purpose of the Study:

  • To present a suite of computational tools for improved cryo-EM map interpretation.
  • To facilitate the generation of stereochemically sound all-atom models from EM data.

Main Methods:

  • Repurposing the BALBES database for protein fold identification from density maps.
  • Modifying Coot with new Jiggle Fit and morphing tools for enhanced EM map interpretation.
  • Extending ProSMART and developing LIBG for generating nucleic acid restraints.

Main Results:

  • Enhanced Coot functionality for handling nucleic acids and interpreting EM maps.
  • Modified REFMAC for optimal atomic model fitting into EM maps.
  • Integrated restraint generation with Coot for real-space and REFMAC for reciprocal-space refinement.

Conclusions:

  • The described tools significantly improve the accuracy and reliability of atomic models derived from cryo-EM data.
  • These advancements aid in stabilizing refinement and reducing overfitting in structural modeling.
  • The integrated workflow streamlines the process of building and refining models from cryo-EM reconstructions.