What is the structural chemistry of the living organism at its temperature and pressure?

The three probes of the structure of matter (X-rays, neutrons and electrons) in biology have complementary properties and strengths. For the study of combined states of order and disorder, NMR crystallography is also applicable. Overall, to understand a biological system, the requirements are physiologically relevant results. Reporting of protein crystal structures, and their associated database entries, could usefully indicate how close to the biological situation they are.

Amyloid structure determination in RELION-3.1

Amyloid structure determination in RELION is increasingly popular, but may suffer from refinements becoming stuck in local minima. This paper describes a new method for initial model generation that may alleviate this problem.

FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

A method is presented to reconstruct the 2D electron densities of fiber cross-sections from disordered small-angle X-ray scattering measurements, combining fiber diffraction theory with physical constraints, like finite cross-section size and non-negative density, in a numerical optimization framework.

Probing the role of the conserved residue Glu166 in a class A β-lactamase using neutron and X-ray protein crystallography

Neutron and X-ray diffraction were used to investigate the effects of a Glu166Gln mutation on the active site of a class A β-lactamase.

The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical di­sulfide pattern and incomplete CWR layers

The first structure of a thrombospondin module 1 (TSP1) domain from a CCN-family matricellular protein has been determined by X-ray crystallography. The structure shows a typical three-stranded fold, but lacks the π-stacked structure that is usually found in these domains. The structure reveals highest conservation in the positively charged central segment, which is predicted to be a binding site for heparan sulfates. The atypical features of this domain have been used to revise the definition of TSP1 domains and to identify a number of new domains in sequence databases.

Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein

Three non-aminoacyl-tRNA synthetase (aaRS) scaffold proteins, AIMP1/p43 (pro-EMAP II), AIMP2/p38 and AIMP3/p18, known as aaRS-interacting multifunctional proteins, are critical in driving the assembly of multi-aaRS complexes in higher eukaryotes. Here, the structural features of the N- and C-terminal domains of the Plasmodium vivax p43 (Pvp43) protein are addressed. A comprehensive structural analyses of the two domains of Pvp43 reveals several notable features which suggest that it is likely to be a soluble, cytosolic protein with a dimeric assembly of its N-terminal GST-like domain that differs from canonical GST dimers.

Noncrystallographic symmetry-constrained map obtained by direct density optimization

A noncrystallographic symmetry-constrained map obtained by direct density optimization is efficient and equivalent to a noncrystallographic symmetry-averaging map. Using the noncrystallographic symmetry-constrained map, the structure of a T = 1 Penaeus vannamei nodavirus shell-domain subviral particle was newly determined by including twinned data.

Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines

A rapid and reliable sample changer, SPACE-II, has been developed at the SPring-8 macromolecular crystallography beamline BL41XU. It enables samples to be exchanged in 16 s, of which its action accounts for only 11 s. Two years of operating SPACE-II demonstrated that the average number of sample exchanges per day was increased by 40% compared with the previous model, and it had an error rate of only 0.089%.

3D domain swapping in the TIM barrel of the α subunit of Streptococcus pneumoniae tryptophan synthase

The structure of Streptococcus pneumoniae TrpA, which is the α subunit of tryptophan synthase, reveals 3D domain swapping, which has never before been observed for a TIM-barrel protein.

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Electronic configurations at distinct metal centers within a metalloprotein may be characterized by inspecting the scattering factors at the X-ray absorption edge. Such experiments may be feasible at XFEL sources, using Bayesian data analysis.