Atomic model building and refinement into high-resolution cryo-EM maps

Bruno Klaholz,Alexander Myasnikov,S Kundhavai Natchiar,Isabelle Hazemann,Hanna Kratzat

doi:10.1038/protex.2017.122

Abstract

Atomic model building and refinement into high-resolution cryo-EM maps

Highlights

With the recent advent of high-resolution cryo electron microscopy \(cryo-EM) it becomes possible and necessary to refine atomic models to high-quality standards, i.e. with a good fit to the map and good geometric parameters like for crystal structures at equivalent resolution
This would not address the position of side-chains or their rotamer conformations, which need to be refined in detail into the map taking into account precise geometrical parameters and refine temperature \(B) factors
The description includes the method for refining chemically modified residues considering that the high-resolution cryo-EM structure of the human ribosome comprises numerous 2’-O-methylations and various base modifications of the rRNA as well as some amino acid methylations

Summary

Introduction

With the recent advent of high-resolution cryo electron microscopy \(cryo-EM) it becomes possible and necessary to refine atomic models to high-quality standards, i.e. with a good fit to the map and good geometric parameters like for crystal structures at equivalent resolution. We provide a protocol for atomic model refinement into high-resolution cryo-EM maps. Once a cryo-EM 3D reconstruction has been refined to the highest possible resolution, atomic model building and refinement against the cryo-EM map can be performed, as described in the following \(Fig. 1).

Results

Conclusion