ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation

ALEPH characterizes the main-chain geometry of small, noncontinuous fragments to flexibly annotate secondary structure, decompose folds, extract libraries and superpose fragments. Secondary and tertiary structure are described through networks of characteristic vectors, which are defined between the centroids of the C^α and carbonyl O atoms in a peptide.

ALIXE: a phase-combination tool for fragment-based molecular replacement

The software ALIXE, which is available as a standalone program as well as integrated into the ARCIMBOLDO programs, combines partial solutions in reciprocal space to increase the signal and reduce the number of intermediate solutions. Its new implementation is faster and can be used by default in the process of phasing with fragments even on modest hardware.

SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses

When phasing cannot be accomplished from a partial polyalanine starting model, extending the model with side chains in a multi-solution way may succeed. SEQUENCE SLIDER implements this approach for use in ARCIMBOLDO.

Measuring and using information gained by observing diffraction data

The information content gained by making a diffraction-intensity measurement is a natural criterion for deciding which data make a useful contribution and which can legitimately be omitted from a calculation.

The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution

A novel method for the enhancement of automated protein model building using polypeptide fragments of homologous structures is presented.

A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study

A practical perspective on molecular-replacement (MR) structure-determination pipelines is presented, using PilA1 from Clostridioides difficile as an example of a difficult case. A manual approach informed by the biology of the system under study is described, together with ab initio MR structure determination.

Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling

The solution of coiled-coil crystal structures may be achieved by AMPLE through the use of ensembled ab initio models in molecular replacement. Improvements in ab initio modelling of elongated helices and oligomeric coiled-coils allow AMPLE to solve a greater number of coiled-coil structures and at lower resolution than previously achieved.

Estimating local protein model quality: prospects for molecular replacement

Local error estimates can be used to improve the success of models in molecular replacement.

Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases

Type 2 cysteine desulfurases are ubiquitous and often essential in plants and microorganisms owing to their role in Fe–S cluster biosynthesis. Here, an X-ray crystal structure of wild-type SufS with a rotated active-site β-hairpin, and a global structure and sequence analysis that argues for a conserved β-latch mechanism regulating type 2 cysteine desulfurases, are reported.

Optimizing the refinement of merohedrally twinned P6₁ HIV-1 protease–inhibitor cocrystal structures

In the present study, it is shown that refinement and the resulting structures of hexagonal HIV-1 protease cocrystal structures can be markedly improved by choosing a lower symmetry space group (P6₁) and applying a twin law (h, −h − k, −l) to correct for merohedral twinning.