Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

J. Appl. Cryst.の発刊に際して

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

/pdf/macromolecular-structure-determination-using-x-rays-neutrons-7udc75ny0s.pdf

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence1. This problem is of fundamental importance as the structure of a protein largely determines its function2; however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures3. Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force4 that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction5 (CASP13)-a blind assessment of the state of the field-AlphaFold created high-accuracy structures (with template modelling (TM) scores6 of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined7.

/pdf/improved-protein-structure-prediction-using-potentials-from-39yatxdc6a.pdf

Improved protein structure prediction using potentials from deep learning

Interpretation of X-ray Powder Diffraction Patterns . By H. Lipson and H. Steeple. Pp. viii + 335 + 3 plates. (Mac-millan: London; St Martins Press: New York, May 1970.) £4.

X-Ray Diffraction

A 3D printed hybrid nozzle device combining a microfluidic mixer with a liquid jet injector that addresses the bottleneck of investigating substrate-initiated biological reaction paths employing serial crystallography with XFELs. The hybrid nozzle provides for injecting aqueous protein crystal jets after fast mixing (<5 ms), reaching reaction time points (e.g., about 10 ms to about 150 ms) suitable to resolve enzyme kinetics.

3d printed microfluidic mixers and nozzles for crystallography

Low-Temperature Scanning Tunneling Microscopy

We demonstrate near-atomic-resolution Bragg diffraction from aerosolized single granulovirus crystals using an x-ray free-electron laser. The form of the aerosol injector is nearly identical to conventional liquid-microjet nozzles, but the x-ray-scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. This approach provides a route to study the weak diffuse or lattice-transform signal arising from small crystals. The high speed of the particles is particularly well suited to upcoming MHz-repetition-rate x-ray free-electron lasers.

/pdf/femtosecond-x-ray-diffraction-from-an-aerosolized-beam-of-4ynp2dzfin.pdf

Femtosecond x-ray diffraction from an aerosolized beam of protein nanocrystals

A PDB code given in Table 2 of Martin-Garcia et al. [ J. Synchrotron Rad. (2022). 29, 896–907] is corrected.

/pdf/serial-macromolecular-crystallography-at-alba-synchrotron-3cfq22qk.pdf

Serial macromolecular crystallography at ALBA Synchrotron Light Source. Erratum

http://absimage.aps.org/image/DFD05/MWS_DFD05-2005-020096.pdf

Uwe Weierstall

Papers

3d printed microfluidic mixers and nozzles for crystallography

Low-Temperature Scanning Tunneling Microscopy

Femtosecond x-ray diffraction from an aerosolized beam of protein nanocrystals

Serial macromolecular crystallography at ALBA Synchrotron Light Source. Erratum

Microscopic Rayleigh Droplet Beams