Archiving raw crystallographic data

An introduction to a collection of articles from the IUCr Diffraction Data Deposition Working Group.

Experiences with making diffraction image data available: what metadata do we need to archive?

A local raw `diffraction data images' archive was made available and some data sets were retrieved and reprocessed, which led to analysis of the anomalous difference densities of two partially occupied Cl atoms in cisplatin as well as a re-evaluation of the resolution cutoff in these diffraction data. General questions on storing raw data are discussed. It is also demonstrated that often one needs unambiguous prior knowledge to read the (binary) detector format and the setup of goniometer geometries.

Operation of the Australian Store.Synchrotron for macromolecular crystallography

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described.

How to make deposition of images a reality

An analysis is performed of the technical and financial challenges to be overcome if deposition of primary experimental data is to become routine.

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible.

Multi-crystal native SAD analysis at 6 keV

Anomalous diffraction signals may be routinely enhanced for native-SAD analysis by merging multi-crystal data sets at 6 keV.

The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes

In the crystal lattice, eight trimers of allophycocyanin B form a porous spherical, 48-subunit assembly, in which the phycocyanobilin chromophore is co-planar.

Solving the RNA polymerase I structural puzzle

Details of the RNA polymerase I crystal structure determination provide a framework for solution of the structures of other multi-subunit complexes. Simple crystallographic experiments are described to extract relevant biological information such as the location of the enzyme active site.

A new family of β-helix proteins with similarities to the polysaccharide lyases

Cthe_2159 is a member of a domain of unknown function family (DUF4353) and was identified from the C. thermocellum genome by its ability to bind cellulose. The structure was determined using gadolinium SAD phasing and shows structural features that are highly similar to some polysaccharide lyase families.

Metrics for comparison of crystallographic maps

Rank scaling of Fourier syntheses leads to new tools for the comparison of crystallographic contour maps. The new metrics are in better agreement with a visual map analysis than the conventional map correlation coefficient.

The structure of a tetrameric α-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular di­sulfides that contribute to its thermostability

The thermostability of the α-carbonic anhydrase from the thermophilic bacterium T. ammonificans is shown to depend on the formation of intrasubunit disulfide bonds and a unique intersubunit disulfide/lysine core at the centre of the tetrameric molecule. Unlike most α-carbonic anhydrases, this enzyme does not show esterase activity towards p-nitrophenyl acetate, which is proposed to be owing to its increased structural rigidity.

Crystal structure and functional implications of LprF from Mycobacterium tuberculosis and M. bovis

The crystal structure of the lipoprotein LprF found in M. tuberculosis and M. bovis has been determined at 1.1 Å resolution.

Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members

Peptidoglycan O-acetylesterase (Ape1), which is required for host survival in Neisseria sp., belongs to the diverse SGNH hydrolase superfamily, which includes important viral and bacterial virulence factors. Here, multi-domain crystal structures of Ape1 with an SGNH catalytic domain and a newly identified putative peptidoglycan-detection module are reported.

Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications

The crystal structure of arabinose-5-phosphate isomerase from B. fragilis NCTC 9343 in complex with an endogenous ligand, CMP-Kdo, is described. Structural and sequence comparisons suggest highly conserved functional residues in the active site that could be targeted for antibacterial drug design.

New methods for indexing multi-lattice diffraction data

A new indexing method is presented which is capable of indexing multiple crystal lattices from narrow wedges of data. The efficacy of this method is demonstrated with both semi-synthetic multi-lattice data and real multi-lattice data recorded from microcrystals of ∼1 µm in size.

Structures of human constitutive nitric oxide synthases

A new crystal structure of the human nNOS heme domain and a better diffracting crystal form of human eNOS heme domain are described.

Low-dose X-ray radiation induces structural alterations in proteins

It is shown that even a low dose (0.06 MGy) of synchrotron radiation absorbed by a protein crystal induces structural alterations. This finding raises a significant issue as it may question previously solved structures as well as highlighting and defining new limitations of protein X-ray crystallography.

A case study on the treatment of protein SIRAS data

A case study on the treatment of SIRAS data using the originally unknown protein LegC3N is described. An iterative direct-method-based treatment was proposed that led to improved results in this particular test case.

Structure of archaerhodopsin-2 at 1.8 Å resolution

The same hexagonal array of archaerhodpsin-2 trimers as observed in the native membrane is reconstituted in a three-dimensional crystal prepared by the membrane fusion method. In this crystal, a pair of conserved glutamate residues in the proton-release pathway is maintained by a low-barrier hydrogen bond.

Using textons to rank crystallization droplets by the likely presence of crystals

A robust and transferable algorithm is presented to objectively describe and rank robotically captured images of crystallization droplets according to their likelihood of crystalline behaviour for the efficient and accurate identification of successful crystallization.

Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1

High-multiplicity data were used to solve the West Nile virus NS1 structure by S-SAD and for the extension of useable resolution for refinement.

Crystallographic study of the phospho­ethanolamine transferase EptC required for polymyxin resistance and motility in Campylobacter jejuni

The C. jejuni phosphoethanolamine transferase EptC functions in antibacterial resistance, motility and host intestinal colonization. In this study, the three-dimensional structure of the catalytic domain of EptC is reported in a covalent phosphoenzyme-intermediate state. EptC active-site mutant strains of C. jejuni demonstrate the potential for EptC enzyme inhibitors.

Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2

The high-resolution crystal structures of the human tankyrase 2 poly(ADP-ribose) polymerase (PARP) domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials.

Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6′)-Ie-APH(2′′)-Ia revealed by crystallographic and small-angle X-ray scattering analysis

The X-ray structure of the N-terminal acetyltransferase domain [AAC(6′)-Ie] of the bifunctional antibiotic-resistance enzyme AAC(6′)-Ie-APH(2′′)-Ia has been determined as a ternary kanamycin/coenzyme A complex. X-ray structures of the isolated AAC(6′)-Ie and APH(2′′)-Ia domains, combined with small-angle X-ray scattering (SAXS) data, allowed the determination of the structural architecture of the full-length bifunctional enzyme in solution.

Human insulin analogues modified at the B26 site reveal a hormone conformation that is undetected in the receptor complex

[AsnB26]- and [GlyB26]-insulin mutants attain a B26-turn like fold without assistance of chemical modifications. Their structures match the insulin receptor interface and expand the spectrum of insulin conformations.

Comment on Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights by Róna et al. (2013)

A comment on the article by Róna et al. [(2013), Acta Cryst. D69, 2495–2505].

Factors influencing nucleo-cytoplasmic trafficking: which matter? Response to Alvisi & Jans' comment on Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights

A response to the article by Alvisi & Jans [(2014), Acta Cryst. D70, 2775_2776].

On the prompt update of literature references in the Protein Data Bank

Updating literature references in the Protein Data Bank is discussed.

Response to On prompt update of literature references in the Protein Data Bank

A response to the article On the prompt update of literature references in the Protein Data Bank [Wlodawer (2014), Acta Cryst. D70, 2779].