An introduction to molecular replacement

An outline is given of the basic features of the molecular-replacement method for solving crystal structures.

AMoRe: classical and modern

An account is given of the latest developments of the AMoRe package.

The befores and afters of molecular replacement

This review outlines questions to consider when attempting to solve crystal structures by molecular replacement.

Sequence alignment for molecular replacement

The problems of gaining accurate protein sequence alignments for molecular replacement are discussed, current techniques explained and strategies suggested.

Model preparation in MOLREP and examples of model improvement using X-ray data

The default model-preparation scheme of MOLREP is described. Two examples are presented of model improvement using X-ray data.

Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis

The possibility of taking into account large-amplitude collective movements of a given model by using a subset of low-frequency normal modes is evaluated for molecular replacement and refinement using X-ray data or cryo-EM maps.

ARP/wARP and molecular replacement: the next generation

A systematic test shows how ARP/wARP deals with automated model building for structures that have been solved by molecular replacement. A description of protocols in the flex-wARP control system and studies of two specific cases are also presented.

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

The highly automated PHENIX AutoBuild wizard is described. The procedure can be applied equally well to phases derived from isomorphous/anomalous and molecular-replacement methods.

Combining X-ray and electron-microscopy data to solve crystal structures

Overview and examples of combined use of X-ray and electron-microscopy data.

From electron microscopy to X-ray crystallography: molecular-replacement case studies

Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement using various standard MR packages such as AMoRe, MOLREP and Phaser.

Fitting molecular fragments into electron density

A number of techniques for the location of small and medium-sized model fragments in experimentally phased electron-density maps are explored. The application of one of these techniques to automated model building is discussed.

NCS-constrained exhaustive search using oligomeric models

Three difficult MR cases are reported in which the orientation of a search oligomer or its internal parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches. Such an exhaustive search was feasible because of constraints on the model parameters derived from the self-rotation function.

Surprises and pitfalls arising from (pseudo)symmetry

The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented.

Type II de­hydroquinase: molecular replacement with many copies

The type II dehydroquinase enzyme is a symmetrical dodecameric protein which crystallizes in either high-symmetry cubic space groups or low-symmetry crystal systems with multiple copies in the asymmetric unit. Both systems have provided challenging examples for molecular replacement; for example, a triclinic crystal form has 16 dodecamers (192 monomers) in the unit cell. Three difficult examples are discussed and two are used as test cases to compare the performance of four commonly used molecular-replacement packages.

MrBUMP: an automated pipeline for molecular replacement

An automation pipeline for macromolecular structure solution by molecular replacement with a special emphasis on the discovery and preparation of a large number of search models is described.

BALBES: a molecular-replacement pipeline

The fully automated pipeline, BALBES, integrates a redesigned hierarchical database of protein structures with their domains and multimeric organization, and solves molecular-replacement problems using only input X-ray and sequence data.

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

The practical limits of molecular replacement can be extended by using several specifically designed protein models based on fold-recognition methods and by exhaustive searches performed in a parallelized pipeline. Updated results from the JCSG MR pipeline, which to date has solved 33 molecular-replacement structures with less than 35% sequence identity to the closest homologue of known structure, are presented.