forthcoming articles

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

See also Forthcoming articles in all IUCr journals.

Accepted 25 November 2015

Mask-based approach to phasing of single-particle diffraction data

A procedure is suggested for ab initio phasing of diffraction data for single-particle studies. The procedure is based on Monte Carlo type search for connected binary masks approximating electron density distribution.

Accepted 24 November 2015

Initiating heavy-atom-based phasing by multi-dimensional molecular replacement

A strategy is presented to set up an n-dimensional molecular-replacement parameter matrix (MRPM) search using anomalous difference Fourier maps from related data sets to uncover weak, but correct, molecular-replacement solutions for heavy-atom substructure determination and subsequent experimental phasing.

Accepted 23 November 2015

A new default restraint library for the protein backbone in PHENIX: a conformation-dependent geometry goes mainstream

The default geometry restraints used in PHENIX for the protein backbone have been upgraded to account for the known conformation dependencies of bond angles and lengths.

Accepted 19 November 2015

Re-refinement of the spliceosomal U4 snRNP core-domain structure

The structure of the spliceosomal U4 snRNP core domain has been re-refined following molecular replacement using the minimal U1 snRNP as a search model. RNA-omit maps show that the U4 Sm-site nucleotides AAUUUUU are bound to the seven Sm proteins SmF–SmE–SmG–SmD3–SmB–SmD1–SmD2 in the same manner as the U1 Sm-site nucleotides AAUUUGU, except at the U-to-G substitution in SmD1.

Accepted 17 November 2015

Efficient merging of data from multiple samples for determination of anomalous substructure

The benefits of using local scaling and optimization of anomalous signal (as implemented in PHENIX) for merging data sets from many crystals for determination of the substructure for weak anomalous scatterers are examined.

Accepted 15 November 2015

Radiation-damage-induced phasing: a case study using UV irradiation with light-emitting diodes

A case study of radiation-damage-induced phasing is discussed using UV-LEDs to induce specific radiation damage.

Accepted 15 November 2015

In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures

A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase at cryogenic temperatures (100 K) is described. It works with nanogram to single-digit microgram quantities of protein and lipid (and ligand when present), and is compatible with both high-resolution native data collection and experimental phasing without the need for crystal harvesting.

Accepted 15 November 2015

Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop

Five crystal structures of D-alanine-D-alanine ligase (DDL) from Y. pestis have been determined at 1.7–2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5′-(β,γ-imido) triphosphate (AMPPNP)-bound and D-alanyl-D-alanine- and ADP-bound structures. The serine loop is mainly responsible for the conformational change in the substrate nucleotide phosphates.

Accepted 14 November 2015

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca2+-calmodulin

Experimental phase information at 1.0 Å resolution was used to validate a more complete multiple conformation model of Ca2+-calmodulin disorder and identified bound 2-methyl-2,4-pentanediol (MPD) in multiple regions of the protein. This bound MPD is likely to contribute to some of the previously noted peculiar features of the Ca2+-calmodulin crystal structure.

Accepted 13 November 2015

Radiation damage and derivatization in macromolecular crystallography: a structure factor's perspective

Both site-specific radiation damage and heavy-atom derivatization result in small changes to the intensity of reflections. The size of change owing to each is calculated and compared for individual reflections.

Accepted 12 November 2015

Lattice filter for processing image data of three-dimensional protein nanocrystals

A specialized filter for lattice finding in images of three-dimensional nanocrystals devoid of any contrast is described.

Accepted 12 November 2015

Structure of the ectodomain of the electron transporter Rv2874 from Mycobacterium tuberculosis reveals a thioredoxin-like domain combined with a carbohydrate-binding module

The structure of the extramembrane portion of the CcdA-family member Rv2874 from M. tuberculosis reveals a previously unseen juxtaposition of a thioredoxin-like domain with a carbohydrate-binding module, suggesting a role in cell-wall carbohydrate processing.

Accepted 11 November 2015

Molecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses

Crystal structures of the C-terminal domains of the Ebolavirus nucleoproteins (NPCt) from the Bundibugyo and Taï Forest species (BDBV and TAFV, respectively) have been determined. The structures show high similarity to that reported for the Zaire Ebolavirus NPCt. However, NMR data revealed that the corresponding domain from the NP of the related MARV species of Marburgvirus is distinctly different.

Accepted 9 November 2015

A technique for the determination of the deuterium/hydrogen contrast map in neutron macromolecular crystallography

The deuterium/hydrogen neutron contrast map, which was calculated using subtraction in real space, demonstrated the powerful detectability of H/D exchange in the neutron structure determination of a ribonuclease A crystal.

Accepted 6 November 2015

The structure of VgrG1 from Pseudomonas aeruginosa, the needle tip of the bacterial type VI secretion system

This article presents the crystal structure of full-length VgrG1 from P. aeruginosa, a component of the type VI secretion-system machinery essential in bacterial infection.

Accepted 2 November 2015

Bacillus licheniformis trehalose-6-phosphate hydrolase structures suggest keys to substrate specificity

Wild-type and mutant structures of B. licheniformis trehalose-6-phosphate hydrolase suggest new insight into the characteristics and substrate specificity of trehalose-6-phosphate hydrolase.

Accepted 13 October 2015

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

Algorithms for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD data set are described.

Accepted 12 October 2015

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing

The useful anomalous correlation and the anomalous signal in a SAD experiment are metrics describing the accuracy of the data and the total information content in a SAD data set and are shown to be related to the probability of solving the anomalous substructure and the quality of initial phases.

Accepted 6 August 2015

A history of experimental phasing in macromolecular crystallography

The development of phasing methods in protein crystallography is presented.

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