Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300

Coma-corrected single-particle data collection on a JEOL CRYO ARM 300 is described. It is shown that data collection with a throughput exceeding 6000 images per day and an image shift of up to 7 µm produces a reconstruction of apoferritin to a resolution of 1.7 Å.

Optimized cryo-EM data-acquisition workflow by sample-thickness determination

Sample thickness is a key parameter in single-particle cryo-electron microscopy. Determining the sample thickness before data acquisition allows the targeting of optimal areas and the maximization of the data-output quality of single-particle cryo-electron microscopy sessions. Scripts and optimized workflows for EPU and SerialEM are presented and are available as open source.

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

A data-processing pipeline to solve structures from tomograms of protein nanocrystals is presented and validated using simulated crystals. The robustness of this workflow to radiation damage is assessed to investigate optimal data-collection strategies.

Structural and functional studies of SAV1707 from Staphylococcus aureus elucidate its distinct metal-dependent activity and a crucial residue for catalysis

Crystal structures of apo and cAMP-bound SAV1707, a member of the UPF0173 metal-dependent hydrolase family from Staphylococcus aureus, were determined at 2.05 and 1.55 Å resolution, respectively, providing functional and structural insights into the catalytic mechanism of SAV1707.

Control of strain in subgrains of protein crystals by the introduction of grown-in dislocations

It is demonstrated that there is a large amount of local strain in subgrains of glucose isomerase crystals even though the overall crystal quality is rather high, as shown by clear equal-thickness fringes in X-ray topography. By controlling the local strain in subgrains, the resistance of subgrains of protein crystals to radiation damage could be improved, enabling the collection of X-ray diffraction data sets with high diffractivity.

Intermediates in allosteric equilibria of DnaK–ATP interactions with substrate peptides

ATP and client peptides interact allosterically to effect the molecular-chaperone activity via which Hsp70 proteins promote protein folding. Here, two DnaK–ATP structures are described: one with implications for a transition in which peptides are released upon the binding of ATP and one with relevance for the rebinding and capture of client polypeptides.

Crystal structures of UDP-N-acetylmuramic acid L-alanine ligase (MurC) from Mycobacterium bovis with and without UDP-N-acetylglucosamine

M. bovis MurC binds UDP-N-acetylglucosamine, the substrate of MurA, and the crystal structure of the complex was determined.

Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography

A highly flexible, integrated system for preparing samples for serial synchrotron crystallography at room and cryogenic temperatures is described and evaluated. The system is compatible with the existing infrastructure for high-throughput crystallography at synchrotrons and addresses major issues in maximizing data quantity and quality from large numbers of small crystals.

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion

An improved antibody-labeling method using an inserted exogenous epitope is presented, in which binding of the antibody has less impact on the folding of the target.

On the suitability of using the diagonal Gaussian approximation in the calculation of the magnitude-based likelihood function

The correlation of structure factors calculated from a random-atom model for reflections s and w is defined by the values of the Fourier transform of the atomic coordinate distribution taken at the 2s, 2w, s − w and s + w nodes and may be large for neighbouring nodes of a reciprocal-space lattice.

Structural basis of chitin utilization by a GH20 β-N-acetylglucosaminidase from Vibrio campbellii strain ATCC BAA-1116

Crystal structures of a GH20 β-N-acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.

Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties

The crystal structures of hemoglobin from two flightless birds, ostrich at 2.22 Å resolution and turkey in a monoclinic form at 1.66 Å resolution and in an orthorhombic form at 1.39 Å resolution, are reported and their sequential and structural features are interpreted.

Notes of a protein crystallographer: the legacy of J.-B. J. Fourier – crystallography, time and beyond

The legacy of J.-B. J. Fourier, a pioneer Egyptologist and premier mathematician and physicist of his time, in crystallography and many other scientific fields is reviewed in the context of nearly two centuries having passed since his landmark publication on The Analytical Theory of Heat (1822). The legacy of Fourier's work in crystallography and many other scientific fields is reviewed with an emphasis on current developments in the study of nonequilibrium thermodynamics.