Non-merohedral twinning: from minerals to proteins

Examples are presented of successful data-processing, phasing and refinement strategies for non-merohedral twins, covering the range from minerals to proteins.

Molecular replacement using structure predictions from databases

Predicted ab initio protein models from online databases are a useful supplement to the PDB for molecular replacement, but usually require nontrivial processing to succeed.

Shake-it-off: a simple ultrasonic cryo-EM specimen-preparation device

A method is presented for high-speed low-volume cryo-EM specimen preparation with a device constructed from readily available components.

Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin

Controlled dehydration experiments have revealed a new crystal form of afamin, a human blood plasma glycoprotein and transporter of hydrophobic molecules. The comparison shows substantial molecular plasticity and amplifies the necessity to examine multiple crystal forms and to refine multiple models, while at the same time the new structure cautions against the interpretation of fatty-acid ligand density in crystals derived from PEGs as major precipitants. An isomorphic low-resolution structure model suggests that afamin is capable of transporting gadoteridol (Gd-DO3A), a magnetic resonance imaging compound.

Identifying dynamic, partially occupied residues using anomalous scattering

Structural studies of partially occupied, heterogeneous protein systems using crystallography are difficult. Here, methods are presented for detecting these states in crystals.

X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions

X-ray crystallographic analyses of deuterated and protiated samples of green fluorescent protein were performed at sub-ångström resolutions in order to compare protonation states, especially around the chromophore.

Structure and mechanism of piperideine-6-carboxylate de­hydrogenase from Streptomyces clavuligerus

High-resolution crystal structures of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus in its apo form and in complexes with the cofactor NAD⁺, the product α-aminoadipic acid and the substrate analogue picolinic acid are described. The data presented provide insights into ligand binding and catalysis.

Comparison of automated crystallographic model-building pipelines

A comparison of four protein model-building pipelines (ARP/wARP, Buccaneer, PHENIX AutoBuild and SHELXE) was performed using data sets from 202 experimentally phased cases, both with the data as observed and truncated to simulate lower resolutions.

Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2′′-phosphotransferases

The structural architecture of the ternary GDP–kanamycin–aminoglycoside-2′′-phosphotransferase IIIa complex reveals no regulation of GTP hydrolysis.

Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose

Crystal structures and the enzymatic properties of the GH6 Orpinomyces sp. Y102 CelC7 enzyme suggest that this enzyme may perform enzymatic hydrolysis in the same way as cellobiohydrolases and endoglucanases.