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opencc-by-4.0Feb 2020View details →

X-ray diffraction data for WD-repeat domain of WDR41

X-ray diffraction data for WD-repeat domain of WDR41 were collected at the APS24IDE beamline on 2019-11-14.

opencc-zeroMay 2020View details →

Data from: The effect of heat treatments on the phase composition and diffraction patterns of goethite to α-Fe2O3/γ-Fe2O3 transformation

Recovered iron hydroxides from Electro-coagulated (EC) sludge collected from the textile wastewater treatment plant and heat treated forms of iron oxides on phase composition properties and phase identification were reported. EC sludges containing iron hydroxides were examined with heat treatment at a temperature of 100, 300, 500 and 800 0C. The raw and analyzed data of the x-ray diffraction examinations of the raw iron hydroxides containing EC sludge and transformed iron oxides were reported. X- ray Diffraction (XRD) analytical techniques were used for both raw EC sludge and transformed iron oxides, hematite, characteristic determination. Iron oxide (Hematite) diffraction pattern as comparative to International Central Diffraction Data (ICDD) from heat treated at high temperature EC sludge were evaluated and confirmed. Raw and analyzed data of XRD analysis for both recovered iron hydroxides and transformed iron oxides is uploded in the data repository as PDF and XPS viewer.

opencc-by-4.0Feb 2020View details →

Neutron powder diffraction data of solid methane in the range 8K-90K

Raw and processed neutron powder diffraction data from solid methane in the range 8K-90K in 2K steps. Data were collected on the Wombat high-intensity powder neutron diffractometer. This data accompanies a submitted publication.

opencc-by-4.0Feb 2020View details →

Neutron powder diffraction data from nitrogen in the range 16K-72K

Neutron powder diffraction data from nitrogen solidified in situ and measured from 16K up to 72K. Data were measured on the Wombat high intensity neutron powder diffractometer at ANSTO, Australia.

opencc-by-4.0Jun 2020View details →

Image and diffractions of a Synthetic-holographic protein

In this dataset are collected the image plane and diffraction patterns of phase Synthetic-Computer generated hologram of a ferritin protein. We designed such holograms to test our OAM sorting system for our future studies on proteins

opencc-zeroAug 2020View details →

In vivo x-ray diffraction and simultaneous EMG reveal the timecourse of myofilament lattice dilation and filament stretch

Muscle function within an organism depends on the feedback between molecular and meter-scale processes. Although the motions of muscle's contractile machinery are well described in isolated preparations, only a handful of experiments have documented the kinematics of the lattice occurring when multi-scale interactions are fully intact. We used time-resolved X-ray diffraction to record the kinematics of the myofilament lattice within a normal operating context: the tethered flight of Manduca sexta. As the primary flight muscles of M. sexta are synchronous, we used these results to reveal the timing of in vivo cross-bridge recruitment, which occurred 24 ms (s.d. 26) following activation. In addition, the thick filaments stretched an average of 0.75% (s.d. 0.32) and thin filaments stretched 1.11% (s.d. 0.65). In contrast to other in vivo preparations, lattice spacing changed an average of 2.72% (s.d. 1.47). Lattice dilation of this magnitude significantly affects shortening velocity and force generation, and filament stretching tunes force generation. While the kinematics were consistent within individual trials, there was extensive variation between trials. Using a mechanism-free machine learning model we searched for patterns within and across trials. Although lattice kinematics were predictable within trials, the model could not create predictions across trials. This indicates that the variability we see across trials may be explained by latent variables occurring in this naturally functioning system. The diverse kinematic combinations we documented mirror muscle's adaptability and may facilitate its robust function in unpredictable conditions.

opencc-by-4.0Sep 2020View details →

Shaped Diffraction Patterns

The Shaped Diffraction Patterns (Shaped DP) dataset is a collection of diffraction patterns for 116,910 materials sampled from 116 space groups. These 116 space groups (out of a total of 230) were selected based on the criterion that each group should be represented by at least 100 materials in the Materials Project (MP) library. The selected space groups include 2 triclinic, 13 monoclinic, 34 orthorhombic, 25 tetragonal, 17 trigonal, 10 hexagonal, and 15 cubic crystal systems.   Please refer to our article as follows:  <ul> <li>Leslie Ching Ow Tiong, Jeongrae Kim, Sang Soo Han and Donghun Kim, "Identification of crystal symmetry from noisy diffraction patterns by a shape analysis and deep learning," npj Computational Materials, 6:196, 2020. (See <a href="https://www.nature.com/articles/s41524-020-00466-5">link</a>).</li> </ul>

opencc-zeroOct 2020View details →

Intrinsic elastic anisotropy of Westerly granite observed by ultrasound measurements, microstructural investigations and neutron diffraction

Westerly granite (WG) has been accepted as an isotropic homogeneous rock. Here we return to WG and observe significant elastic anisotropy using multidirectional ultrasonic sounding on spherical samples at pressures up to 400 MPa. Thermal treatment of WG leads to formation of microcracks that reduce elastic wave velocities and increase its elastic anisotropy. The 3D distribution of P-wave velocities at low pressure is close to orthorhombic symmetry. Application of hydrostatic pressure closes most of thermally induced microcracks and decreases elastic anisotropy of WG, but at high pressure the anisotropy is practically reversed compared to low pressure: maximum P-wave velocity direction at low pressures is near minimum velocity direction at high pressure and vice versa. To understand this effect, microstructures of the rock were investigated by optical and scanning electron microscopy. Preferred orientations of four major rock-forming minerals – quartz, orthoclase, plagioclase and biotite – were measured by time-of-flight neutron diffraction, which confirms significant crystal alignment. All these data were used to numerically model anisotropic elastic properties of WG. It is shown that WG possesses weak intrinsic elastic anisotropy related mainly to the preferred orientation of feldspars formed during igneous crystallization. Observed microcracks are mostly related to the cleavage planes of feldspars and biotite, and thus also demonstrate preferred orientation. Higher preheating temperatures produce larger quantity of longer microcracks. These microcracks act against the weak intrinsic elastic anisotropy of WG, and define the elastic anisotropy at low pressures.

opencc-by-sa-4.0Nov 2020View details →

Data for "TrueEBSD: correcting spatial distortions in electron backscatter diffraction maps"

Data for "TrueEBSD: correcting spatial distortions in electron backscatter diffraction maps" published in Ultramicroscopy. Journal DOI: <a href="https://doi.org/10.1016/j.ultramic.2020.113130">https://doi.org/10.1016/j.ultramic.2020.113130</a>; Preprint DOI: <a href="https://arxiv.org/abs/1909.00347">https://arxiv.org/abs/1909.00347</a>. The zipped folder contains: <ol> <li>Readme (text file)</li> <li>'Ti-64' data subfolder: data for one of the maps in the Ti-64 map stitching example</li> <li>'ZrH' data subfolder: data for the hydride-containing Zircaloy-4 example</li> <li>'CP-Zr' data subfolder: data for the in-situ deformed Zr example</li> <li> 'MATLAB scripts' subfolder: TrueEBSD source code.</li> </ol>   Each data subfolder contains: <ul> <li>Input image files</li> <li>EBSD orientation files in Bruker CTF format</li> <li>'Outputs' subfolder containing output figures as image files.</li> </ul> The 'MATLAB scripts' subfolder contains TrueEBSD source code: <ul> <li>The primary user interface is 'input_deck.m'. Most user settings can be changed here. <ul> <li>The input deck entries here have been pre-filled for the Ti-64 dataset.</li> </ul> </li> <li>To use TrueEBSD, run 'input_deck.m' in MATLAB.</li> <li>The method is outlined in 'main.m', which calls functions in 'MATLAB scripts\code\'.</li> </ul>

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group C2)

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group C2). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV9">7AV9</a>.   Additional information: dataset: PHIPA-x1724 beamline: Diamond Light Source I04-1 visit:  nt11175-63 date: 16-04-2015 Ω Start: 144.0° Ω Osc: 0.12° Ω Overlap: 0° No. Images: 1500 Resolution: 1.50Å Wavelength: 0.9173Å Exposure: 0.040s Transmission: 100.00% Beamsize: 60x50μm

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P212121)

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P212121). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7BBO">7BBO</a>.   Additional information: dataset: PHIPA-x1738 beamline: Diamond Light Source I04-1 visit:  nt11175-63 date: 16-04-2015 Ω Start: 90.0° Ω Osc: 0.12° Ω Overlap: 0° No. Images: 1500 Resolution: 1.50Å Wavelength: 0.9173Å Exposure: 0.040s Transmission: 100.00% Beamsize: 60x50μm

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac. The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7BBP">7BBP</a>.   Additional information: dataset: PHIPA-x2179 beamline: Diamond Light Source I04-1 visit:  mx10619-76 date: 20-06-2016 Ω Start: 216.3° Ω Osc: 0.15° Ω Overlap: 0° No. Images: 1200 Resolution: 2.00Å Wavelength: 0.9282Å Exposure: 0.050s Transmission: 100.00%

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group p21212)

Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group p21212). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV8">7AV8</a>. Additional information: dataset: PHIPA-x152 beamline: Diamond Light Source I04-1 visit:  mx8421-63 date: 02-03-2014 Ω Start: 90.0° Ω Osc: 0.10° Ω Overlap: 0° No. Images: 1800 Resolution: 1.50Å Wavelength: 0.9200Å Exposure: 0.050s Transmission: 100.00% Beamsize: 60x50μm

opencc-zeroDec 2019View details →

Data from: Making soil particle size analysis by laser diffraction compatible with standard soil texture determination methods

The standard sieving, pipette and hydrometer methods for soil particle size analysis (PSA) have three main drawbacks: procedures are tedious, time-consuming, and the results are protocol-dependent. Laser diffraction PSA delivers rapid results using standardized procedures, but so far it has been difficult to reconcile results with those from standard sedimentation methods. The objective of this study was to develop a protocol that would permit direct usage of laser diffraction PSA and render results compatible with current methods. The protocol was developed using standard soil samples from different textural classes. Regression of the laser diffraction PSA against the hydrometer/pipette method yielded coefficients of determination of 0.92/0.9, 0.92/0.94 and 0.99/0.99, and root mean square errors of 0.04/0.05, 0.07/0.06 and 0.05/0.03 for clay, silt and sand, respectively. These statistics are comparable to those obtained by regressing results of the hydrometer against the sieve and pipette methods. A key factor in securing accurate and precise results was limiting the particle size range of the samples by wet sieving the sand fraction. This created representative samples and stable soil dispersed suspensions, allowing accurate estimations of particle size distribution for clay and silt fractions without empirical transformations. Results obtained with the proposed protocol matched those of standard sedimentation analyses for a wide range of soils, encouraging further adoption of laser diffraction for soil PSA.

opencc-zeroMay 2016View details →

Raw diffraction images of a crystal of thermolysin solved by SAD from data collected by Direct Data Collection (DDC) using the ESRF RoboDiff goniometer

In order to demonstrate the data collection capabilities of the RoboDiff diffraction data were collected from a crystal of thermolysin to demonstrate the suitability of the beamline MASSIF-1 and RoboDiff for ab initio phasing experiments using diffraction data collected at wavelengths at or remote from the absorption edges of the anomalous scattering elements contained in crystals.

openother-pdMay 2016View details →

Diffraction images for 5-aminolevulinic acid dehydratase (ALAD) from E. coli complexed with porphobilinogen.

The diffraction images which allowed the 2.1 Angstrom resolution structure determination of Escherichia coli ALAD co-crystallised with a non-covalently bound moiety of the product, porphobilinogen (PBG), are presented. The structure revealed that the pyrrole side chain amino group is datively bound to the active site zinc ion and that the PBG carboxylates interact with the enzyme via hydrogen bonds and salt-bridges with invariant residues. A number of hydrogen bond interactions that were previously observed in the structure of yeast ALAD with a cyclic intermediate resembling the product PBG appear to be weaker in the new structure suggesting that these interactions are only optimal in the transition state.

opencc-zeroMay 2016View details →

Raw diffraction images of a crystal of Bovine trypsin collected by Direct Data Collection (DDC) using the ESRF RoboDiff goniometer

In order to demonstrate the data collection capabilities of the RoboDiff diffraction data were collected from a crystal of Bovine trypsin to demonstrate the suitability of the beamline MASSIF-1 and RoboDiff for standard data collection.

opencc-zeroMay 2016View details →

Raw diffraction images of a crystal of Ferulic Acid Esterase (FAE) solved by SAD from data collected by Direct Data Collection (DDC) using the ESRF RoboDiff goniometer

In order to demonstrate the data collection capabilities of the RoboDiff diffraction data were collected from a crystal of FAE to demonstrate the suitability of the beamline MASSIF-1 and RoboDiff for ab initio phasing experiments using diffraction data collected at wavelengths at or remote from the absorption edges of the anomalous scattering elements contained in crystals.

openother-pdJun 2016View details →

Diffraction images for Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase.

Diffraction data used to determine the octameric structure of the zinc-dependent ALAD from the hyperthermophile Pyrobaculum calidifontis at a resolution of 3.5 Å.