Improvement of cryo-EM maps by density modification.

Thomas C Terwilliger,Randy J Read,Steven J Ludtke,Paul D Adams,Pavel V Afonine

doi:10.1038/s41592-020-0914-9

Abstract

A density modification procedure for improving maps from single-particle electron cryo-microscopy is presented. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Key differences from applications in crystallography are that the errors in Fourier coefficients are largely in the phases in crystallography but in both phases and amplitudes in electron cryo-microscopy, and that half-maps with independent errors are available in electron cryo-microscopy. These differences lead to a distinct approach for combination of information from starting maps with information obtained in the density modification process. The density modification procedure was applied to a set of 104 datasets and improved map-model correlation and increased the visibility of details in many of the maps. The procedure requires two unmasked half-maps and a sequence file or other source of information on the volume of the macromolecule that has been imaged.

Highlights

Single-particle electron cryo-microscopy is rapidly becoming the dominant technique for determination of large three-dimensional structures of macromolecules and their complexes[1]
The result of a cryo-EM analysis is a three-dimensional map reflecting the electric potential of the macromolecule[2] and which has map values and an appearance closely related to maps obtained from X-ray crystallography[3]
The macromolecule typically occupies only a small part of the volume of the reconstruction, and during reconstruction noise is removed from the part of the map that is outside the macromolecule[8,9]. This can improve the map in the region of the macromolecule and is related to the “solvent flattening” aspect of crystallographic density modification[10]

Summary

Introduction

Single-particle electron cryo-microscopy (cryo-EM) is rapidly becoming the dominant technique for determination of large three-dimensional structures of macromolecules and their complexes[1]. The result of a cryo-EM analysis is a three-dimensional map reflecting the electric potential of the macromolecule[2] and which has map values and an appearance closely related to maps obtained from X-ray crystallography[3]. In both cryo-EM and in macromolecular crystallography, the accuracy of the map is an important characteristic. The macromolecule typically occupies only a small part of the volume of the reconstruction, and during reconstruction noise is removed from the part of the map that is outside the macromolecule[8,9] This can improve the map in the region of the macromolecule and is related to the “solvent flattening” aspect of crystallographic density modification[10]. We show that a version of density modification with the same theoretical basis as crystallographic density modification but with key differences reflecting the differences between crystallographic and cryo-EM maps can be used to improve cryo-EM maps

Methods

Results

Conclusion