Refinement of Atomic Structures Against cryo-EM Maps

Methods Enzymol. 2016;579:277-305. doi: 10.1016/bs.mie.2016.05.033. Epub 2016 Jun 24.

Abstract

This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models.

Keywords: Atomic structure refinement; Bayesian statistics; Best map calculation; Crystallographic maps; Electron scattering; Form factors; Sharpening and blurring; X-ray diffraction.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Bayes Theorem
  • Cryoelectron Microscopy / instrumentation
  • Cryoelectron Microscopy / methods*
  • Crystallography, X-Ray
  • Image Processing, Computer-Assisted / methods
  • Image Processing, Computer-Assisted / statistics & numerical data*
  • Imaging, Three-Dimensional / instrumentation
  • Imaging, Three-Dimensional / methods
  • Models, Molecular
  • Protein Conformation
  • Proteins / ultrastructure
  • Software*
  • X-Ray Diffraction

Substances

  • Proteins