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 8 February 2016

A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction

A more streamlined pipeline for structure determination is described that applies in cellulo X-ray diffraction analysis to crystal-containing cells isolated by flow cytometry. Application of this pipeline to in vivo crystals of the recombinant CPV1 polyhedrin shows that in cellulo analysis is more efficient; compatible with experimental phasing; and does not compromise the quality of the final model.

Accepted 4 February 2016

Diffraction geometry refinement in the DIALS framework

A comprehensive description of methods used within the DIALS\xspace framework for diffraction geometry refinement using predicted reflection centroids is given. Examples of the advanced features of the software are provided.

Accepted 2 February 2016

Phase improvement via Phantom Derivative techniques: ancils that are related with the target structure

Ancil structures correlated with the target structures are used to improve phases via the Phantom Derivative approach.

Accepted 28 January 2016

T-to-R switch of muscle FBPase involves fundamental changes of secondary and quaternary structure

When crystallized in the absence of the allosteric inhibitor AMP, human muscle FBPase has a totally unexpected quaternary structure of its active R form, with the two dimers of the homotetrameric molecule in perpendicular orientation, in stark contrast to the coplanar arrangement of the closely related liver isozyme. The T-to-R switch of the muscle enzyme also involves a highly unusual α→β refolding of the N terminus.

Accepted 25 January 2016

New conformations of linear polyubiquitin chains by crystallographic and solution-scattering studies expand the conformational space of polyubiquitin

A new crystal structure of linear Ub2 reveals a more compact conformation than the previously known conformations. Solution conformations of linear Ub2, Ub3 and Ub4 were probed by small-angle X-ray scattering, revealing that linear Ub3 predominantly adopts compact conformations while linear Ub2 and Ub4 adopt extended conformation. The results provide a full view of the conformational diversity of linear polyubiquitins.

Accepted 25 January 2016

Transmission electron microscopy for the evaluation and optimization of crystal growth

In this communication, we demonstrate the potential of transmission electron microscopy to assist in the process of generating well diffracting crystals for conventional crystallography, as well as free electron laser and micro-electron diffraction applications.

Accepted 23 January 2016

Microcrystal delivery by pulsed liquid droplet for serial femtosecond crystallography

A liquid-droplet injector delivers microcrystals of lysozyme in a pulse-by-pulse manner for conducting serial femtosecond crystallography with an X-ray free-electron laser. The structure was determined at a resolution of 2.3 Å with low sample consumption.

Accepted 22 January 2016

Grappling with anisotropic data, pseudo-merohedral twinning and pseudo-translational noncrystallographic symmetry: a case study involving pyruvate kinase

A clear narrative of complex structure determination, including crystallographic problems of pseudo-merohedral twinning, pseudo-translational symmetry and data anisotropy, is provided. This manuscript provides a description of how these issues encountered during the structural determination of E. coli type 1 pyruvate kinase to 2.28 Å resolution were overcome.

Accepted 19 January 2016

Tackling the crystallographic structure determination of the COP9 signalosome

The low-resolution structure determination of the COP9 signalosome, a large multi-protein complex, from crystals affected by rotational pseudo-symmetry and twinning is detailed.

Accepted 19 January 2016

Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants

Variants of the C—C bond-forming enzymes transaldolase B and D-fructose-6-phosphate aldolase A are irreversibly inhibited by D-tagatose-6-phosphate. A novel structure of a covalently bound ring sugar at the active-site lysine residue of the transaldolase B F178Y variant is revealed.

Accepted 19 January 2016

Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry

The crystal structure of a 32-base-pair RNA double helix (675 non-H atoms) from a trypanosome RNA-editing substrate was determined with 1.05 Å resolution X-ray diffraction data starting from random phases using the direct-methods computer program SIR2014. Success was achieved in the presence of two levels of imperfect translation pseudosymmetry caused by three helical repeats.

Accepted 19 January 2016

Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex

Crystal structures of the cleavage complexes of topoisomerase IV from Gram-negative (K. pneumoniae) and Gram-positive (S. pneumoniae) bacterial pathogens stabilized by the clinically important antibacterial drug levofloxacin are presented, analysed and compared. For K. pneumoniae, this is the first high-resolution cleavage complex structure to be reported.

Accepted 19 January 2016

UHM–ULM interactions in the splicing factor RBM39–U2AF65 complex

The first crystal structure of the RBM39-UHM–U2AF65-ULM complex has been determined at 2.2 Å resolution. Comparison to other UHM−ULM complexes reveals both common and unique interactions.

Accepted 18 January 2016

In-vacuum long-wavelength macromolecular crystallography

The motivation for, and the first results from, the novel in-vacuum long-wavelength MX beamline I23 at Diamond Light Source are presented.

Accepted 18 January 2016

Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines

Best practices in data collection for experimental phasing at the ESRF Structural Biology beamlines are described.

Accepted 16 January 2016

Automated harvesting and processing of protein crystals through laser photoablation

New methods for crystal mounting, soaking and cryocooling contribute to bridging the automation gap between crystallization and X-ray data collection.

Accepted 15 January 2016

Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding. Corrigendum

Accepted 8 January 2016

An overview of heavy-atom derivatization of protein crystals

This review summarizes the reasons why the heavy-atom derivatization of protein crystals can be useful, how to select heavy atoms, how to produce a heavy-atom-modified crystal that still diffracts and how to determine whether the protein has been modified.

Accepted 15 December 2015

Data-collection strategy for challenging native SAD phasing

The successful structure solution of the integral membrane diacylglycerol kinase and the CRISPR-associated endonuclease RNA–DNA complex by native SAD phasing is demonstrated. The structures were solved with a combined low-dose multi-orientation, multi-crystal data-collection strategy.

Accepted 25 November 2015

Phasing and structure of bestrophin-1: a case study in the use of heavy-atom cluster compounds with multi-subunit transmembrane proteins

The structure of a eukaryotic ion channel solved using tantalum bromide SAD phasing is discussed in the context of basic challenges common to membrane proteins.

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 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 ultraviolet light-emitting diodes to induce specific radiation damage.

Accepted 14 November 2015

Using selenome­thionyl derivatives to assign sequence in low-resolution structures of the AP2 clathrin adaptor

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 the change owing to each is calculated and compared for individual reflections.

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