Pink beam crystallography demonstrated in SFX

Nass et al. [IUCrJ (2021), 8, 905–920] applied a wide bandwidth beam (pink beam) to serial femtosecond crystallography at X-ray free electron lasers. This approach will lead to better datasets in a shorter time from fewer crystals.

Mapping completeness

Tchoń & Makal [IUCrJ (2021), 8, 1006–1017] use numerical simulations to explore the dependence of data completeness on crystal orientation, X-ray energy and diamond anvil cell geometry for high-pressure diffraction experiments. Their completeness heat maps for different Laue classes can be used to guide optimization of high-pressure single-crystal diffraction experiments.

virusMED: your travel guide to the virus world

As we respond to viral epidemics and accelerate the discovery of new viruses, sifting through vast volumes of structural virology data could rapidly become an impossible task. virusMED is a curated atlas of metal/drug-binding and immunological hotspots in viral protein structures that provides a navigation guide for structure–function analysis and the development of antiviral strategies.

Revealing the early stages of carbamazepine crystallization by cryoTEM and 3D electron diffraction

A time-resolved crystallization study of early-stage carbamazepine crystallization by cryoTEM reveals two crystallization pathways, one classical and the other non-classical. Four forms of carbamazepine are also identified via 3D electron diffraction from a single crystallization.

High-resolution single-particle cryo-EM of samples vitrified in boiling nitro­gen

Samples for single-particle cryo-electron microscopy can be routinely vitrified using only liquid nitro­gen at its boiling temperature, allowing sample handling workflows to be simplified and sample stresses that contribute to beam-induced motion to be reduced.

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Single-millisecond mix-and-inject experiments are presented on ligand binding to an enzyme performed at the European Free-Electron Laser with high X-ray repetition rates.

Experimental evidence for the benefits of higher X-ray energies for macromolecular crystallography

Higher X-ray energies are experimentally demonstrated to be highly beneficial for macromolecular crystallography.

Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser

Large-bandwidth X-ray free-electron laser pulses significantly reduce sample and beam-time quantities required for obtaining accurate structure-factor amplitudes in serial femtosecond crystallography.

Molecular basis of dimerization of lytic transglycosylase revealed by the crystal structure of MltA from Acinetobacter baumannii

MltA from the human pathogen Acinetobacter baumannii was characterized and its dimeric crystal structure was unveiled, demonstrating the extra-domain-mediated dimerization of MltA for the first time. Based on the current structural and biochemical studies, the working mechanism of MltA with various functionally related proteins on the bacterial outer membrane was modeled.

virusMED: an atlas of hotspots of viral proteins

virusMED (Virus Metal binding sites, Epitopes and Drug binding sites) is a rich internet application based on a database of atomic interactions around hotspots in 7041 experimentally determined viral protein structures.

Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation

This work describes cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation, and by introducing the `frozen plasmon' method. Combined with a coarse-grained all-atom solvent model, this accurately models inelastic scattering effects leading to radiation damage, solvent motion and contrast loss.

Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state

Crystal structures of oxy–deoxy intermediates of a 400 kDa giant hemoglobin reveal the allosteric transition intermediates of the unmodified protein and unrestrained oxygen saturation, which have been missing pieces in the study of the allosteric behavior of hemoglobins over the last half century.

Locating hydrogen positions in the autunite mineral metatorbernite [Cu(UO₂)₂(PO₄)₂·8H₂O]: a combined approach using neutron powder diffraction and computational modelling

A combination of neutron powder diffraction and ab initio random structure searching was used to locate hydrogen positions in the crystal structure of metatorbernite [Cu(UO₂)₂(PO₄)₂·8H₂O], a common autunite mineral that shows promise for uranium remediation.

Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography

Understanding the catalytic mechanism of SARS-CoV-2 main protease (M^pro) can help in guiding drug design of specific small-molecule antivirals. A 2.0 Å resolution room-temperature X-ray crystal structure of inactive C145A mutant M^pro in complex with the octapeptide Ac-SAVLQSGF-CONH₂ that resembles a Michaelis complex is reported.

Comparison of EMC and CM methods for orienting diffraction images in single-particle imaging experiments

Two orientation methods are compared: the expansion maximization compression (EMC) algorithm and the correlation maximization (CM) algorithm. To investigate the efficiency, reliability and accuracy of the methods at various X-ray free-electron-laser pulse fluences, simulated diffraction patterns of biological molecules are used.

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

A new tool based on 3D Zernike polynomials is presented that allows the study of the continuous heterogeneity of biological macromolecules, revealing the structural relationships present among different states by the approximation of deformation fields.

Maximizing completeness in single-crystal high-pressure diffraction experiments: phase transitions in 2°AP

The influence of a diamond anvil cell (DAC) aperture, incident radiation wavelength and sample orientation in a DAC on the completeness of diffraction data collected at high pressure has been systematically analyzed. The considerable impact of sample orientation on achievable data completeness has been confirmed and quantified for all Laue classes in the form of graphical guides. These guides have been applied to predict sample orientation for structural analysis of a sample undergoing an orthorhombic → monoclinic phase transition under pressure which ensured over 90% completeness.

AA_h BN crystal, basic structure of boron nitride nanotubes

For the first time, AA_h boron nitride (BN) crystal, assigned to an orthorhombic space group (No. 31, Pm2₁), is reported. The structure of BN nanotubes is reinterpreted as a helix, resulting from texture and helical growth of the AA_h BN crystal used.

Time scale of glycation in collagen of bovine pericardium-derived bio-tissues

Many pathological side-effects of diabetes and aging are directly linked to non-enzymatic glycation of collagen as an abundant, multi-purpose tissue in human beings. We describe a model that quantifies glycation and its structural effects as a function of sugar level (glucose and ribose) and time, based on SAXS and WAXS data.