Proceedings of the third CCP-EM Spring Symposium

An introduction to the proceedings of the third CCP-EM Spring Symposium.

Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM

REFMAC5 and related tools for the refinement of atomic models into cryo-EM reconstructions in CCP-EM are reviewed. An upper bound on the correlation between observed and calculated Fourier coefficients is identified, and the practical utility of map blurring/sharpening is discussed. The Divide and Conquer pipeline for refining large complexes in parallel, and ProSHADE for the identification of symmetries in a given map or coordinate set, are presented.

Electron diffraction data processing with DIALS

Adaptations to the DIALS package are described that make it a suitable choice for processing challenging continuous-rotation electron diffraction data. The results of using the extended package are presented for a case consisting of seven example data sets.

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

ISOLDE is an interactive molecular-dynamics environment for rebuilding models against experimental cryo-EM or crystallographic maps. Analysis of its results reinforces the need for great care when validating models built into low-resolution data.

Real-space refinement in PHENIX for cryo-EM and crystallography

A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models.

Automated map sharpening by maximization of detail and connectivity

A procedure for optimizing the sharpening of a map based on maximizing the level of detail and connectivity of the map has been developed and applied to 361 pairs of deposited cryo-EM maps and associated models.

Approaches to altering particle distributions in cryo-electron microscopy sample preparation

This paper describes different approaches that cryo-EM users can take to improve the quality of their sample distribution and ice for high-resolution single-particle cryo-EM.

Microtubule architecture in vitro and in cells revealed by cryo-electron tomography

Electron microscopy is a key methodology for studying microtubule structure and organization. Here, the results of cryo-electron tomography experiments on in vitro-polymerized microtubules and comparisons with microtubule ultrastructure in cells are described.

Insights into the evolution of bacterial flagellar motors from high-throughput in situ electron cryotomography and subtomogram averaging

The use of high-throughput in situ electron cryotomography and subtomogram averaging to study the the architecture and diversity of the bacterial flagellar motor is reviewed. Together with phenotypic analysis, this information can be used to better understand the evolution of molecular machines.