forthcoming articles

The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Structural Biology.

See also Forthcoming articles in all IUCr journals.

Accepted 13 January 2017

The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

Small-molecule crystal structures are of tremendous value in understanding protein–ligand complexes, both individually and as a collection.

Accepted 13 January 2017

Dissecting random and systematic differences between noisy composite data sets

A multidimensional scaling analysis of the pairwise correlation coefficients is presented which positions datasets in a sphere with radius one of an abstract, low-dimensional space at radii inversely proportional to their levels of random error, and at spherical angles related to their mutual systematic differences. This dimensionality reduction can not only be used for classification purposes, but also to derive dataset relations on a continuous scale.

Accepted 12 January 2017

Data mining of iron(II) and iron(III) bond valence parameters, and their relevance for macromolecular crystallography

Using all available metal-containing organic compound structures in the Cambridge Structural Database, we developed a novel data-driven method to derive bond valence R0 parameters. While confirming almost all reference literature values, we observe two distinct populations of Fe(II)-N and Fe(III)-N bonds which we interpret as low and high spin states of the coordinating iron. Based on the R0 parameters derived herein, we suggest guidelines for the modeling of iron-ligand distances in macromolecular structures.

Accepted 3 January 2017

AceDRG: a stereochemical description generator for ligands

The program AceDRG generates accurate stereochemical descriptions, and one or more conformations, of a given ligand. The program also analyses entries and extracts local environment-dependent atom types, bonds and angles from the Crystallography Open Database.

Accepted 3 January 2017

Validation and extraction of molecular-geometry information from small-molecular databases

The entries from a freely available small-molecule database, the Crystallography Open Database, have been validated and a reliable subset of the molecules has been selected for the extraction of molecular-geometry information. The atom types and corresponding bond and angle classes derived from this database have been subjected to validation, the results of which are used by AceDRG in the derivation of new ligand descriptions.

Accepted 2 January 2017

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

The structure of an Hfq homolog from the deep-branching thermophilic bacterium A. aeolicus, determined to 1.5 Å resolution both in the apo form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer.

Accepted 21 December 2016

Guidelines for the successful generation of protein–ligand complex crystals

This article aims to guide efforts in protein–ligand complex crystal structure generation, with special consideration of protein-construct design, and summarizes different approaches to co-crystallization and crystal soaking. Common problems and pitfalls are highlighted.

Accepted 21 December 2016

Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry

H atoms are `hard to see' in X-ray crystal structures of protein–ligand complexes. This paper discusses the problem of identifying the correct tautomeric form(s) of protein-bound ligands.

Accepted 20 December 2016

The XChemExplorer graphical workflow tool for routine or large-scale protein–ligand structure determination

XChemExplorer is a graphical workflow and data-management tool for the parallel determination of protein–ligand complexes. Its implementation, usage and application are described here.

Accepted 19 December 2016

Ligand fitting with CCP4

The process of ligand fitting with CCP4 is reviewed, including identifying ligand density in the map, ligand fitting, refinement and subsequent validation. Recent developments are discussed, and are illustrated using instructive examples demonstrating practical application.

Accepted 2 December 2016

A pipeline approach to single-particle processing in RELION

The formal description of a workflow to cryo-EM structure determination in the RELION program allows standardization of procedures and on-the-fly image processing during data acquisition.

Accepted 14 November 2016

Polder maps: improving OMIT maps by excluding bulk solvent

Residual OMIT maps can be improved by the selective exclusion of bulk solvent from the OMIT region.

Accepted 8 November 2016

Keep it together: restraints in crystallographic refinement of macromolecule–ligand complexes

An overview of the process of ligand restraint generation for macromolecular crystallographic refinement is given.

Accepted 21 October 2016

Strategies for carbohydrate model building, refinement and validation

This article addresses many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.

Accepted 17 October 2016

An editor for the generation and customization of geometry restraints

Obtaining a restraint dictionary for novel ligands or improving restraints for known ligands can require their manual modification. This can be tedious and error-prone. REEL is a restraints editor that provides quick, easy and accurate development, allowing global changes and fine-tuning of individual restraints.

Accepted 13 October 2016

Combining X-ray and neutron crystallography with spectroscopy

The use of neutron crystallography and in situ spectroscopy to study enzyme mechanism is discussed.

Accepted 12 October 2016

Twilight reloaded: the peptide experience

The potential causes of the severe misinterpretation of peptide density in a significant number of protein–peptide complex structures are analyzed, together with suggestions for good practice and specific education aimed at minimizing overinterpretation and mistakes in protein–peptide complex structure models.

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