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689 results for “crystals”
Protonation state of proteins in crystals (CpHMD simulations)
<p>Input files to run simulations for:</p> <p>"What is the protonation state of proteins in crystals: insights from constant pH molecular dynamics simulations"</p> <p>by Noora Aho*<strong>†</strong><em>, </em>Gerrit Groenhof*<em>, </em>and Pavel Buslaev* (manuscript submitted in August 2024)</p> <p>*Nanoscience Center and Department of Chemistry, University of Jyväskylä, Finland</p> <p><strong>†</strong>Theoretical Physics and Center for Biophysics, Saarland University, Germany</p> <p> </p>
Compilation of LCF and TMF Data for Single-Crystal and Directionally-Solidified Ni-base Superalloys (All Orientations)
<p>This Excel file contains a compilation of low cycle fatigue (LCF) and thermomechanical fatigue (TMF) data for single-crystal (SX) and directionally-solidified (DS) Ni-base superalloys that are typically used for blades and vanes in gas turbines. Most of the data is generated by strain-controlled uniaxial fatigue tests. Both continuous cycling and cycles with dwells (hold times) at either the maximum or minimum of the cycle are included in the dataset.</p> <p>Several different alloys with similar mechanical behaviors are included in the dataset. The dataset only includes materials that have undergone a solution and age heat treatment typical of that applied to blade and vane components. All the fatigue data in this dataset is limited to uniaxial cyclic loading. The loading direction with respect to the crystal orientation or solidification direction varies. The data in this dataset has been extracted from the public domain. The sources of the data are included in the Excel file.</p> <p>This data is used to train a Probabilistic Physics-guided Neural Network (PPgNN) that outputs a strain-life curve, including the mean response and 95% confidence intervals. The INPUTS and OUTPUTS used in the PPgNN are highlighted in the Excel file.</p>
Crystallization of USP5 Zf-UBD
<p>Determination of crystallization conditions which allow growth of well-diffracting apo crystals of the USP5 zinc finger ubiquitin binding domain (Zf-UBD) </p>
Crystallization of USP5 Zf-UBD #2
<p>Determination of crystallization conditions which allow growth of well diffracting apo crystals of USP5 zinc finger ubiquitin binding domain (Zf-UBD) permissible to soaking with small molecule ligands and optimization and assessment of cryo-protective conditions and DMSO tolerance of these crystals.</p>
Single Crystal X-ray diffraction data for Mycobacterium tuberculosis BioA
<p>Single crystal X-ray diffraction data for MtBioA related to PDBID: xxxx</p> <p>Data collected at Diamond Light Source, UK</p> <p>Beamline I03</p>
Data set for "Chiral Magnonic Crystals: Unconventional Spin-Wave Phenomena Induced by a Periodic Dzyaloshinskii-Moriya Interaction"
<p>Scripts for the micromagnetic simulations of the publication "Chiral Magnonic Crystals: Unconventional Spin-Wave Phenomena Induced by a Periodic Dzyaloshinskii-Moriya Interaction", using the OOMMF software. These codes reproduce the result of magnonic waveguides with periodic Dzyaloshinskii-Moriya interactions. A Dockerfile and a Makefile are included for the reproducibility of the results.</p> <p>The repository containing these results, together with a explanatory README document can be found in:</p> <p>https://github.com/davidcortesortuno/paper-2018-chiral_magnonic_crystals</p> <p> </p> <p>The files included in this Zenodo release refer to the v1.0 version of the data set. For an updated version of the scripts refer to the Github repository.</p>
Eiger HDF5 protein crystal diffraction images of TTR-Pt
<p>These data will be used during the Pasteur Course 3rd Integrative Structural Biology 2018 MX tutorials.</p> <p>The sequence of the protein is (127 amino acids, MW 13.76 kDa):</p> <p>> TTR<br> GPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLT<br> TEEEFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYST<br> TAVVTNPKE</p> <p> </p> <p>There are 5 main platinum sites.</p>
Co-crystal structures of USP5 Zf-UBD and weak binding compounds
<p>Determination of crystallization conditions which allow growth of well-diffracting co-crystals of USP5 zinc finger ubiquitin binding domain (Zf-UBD) and compounds shown to bind weakly by <a href="https://zenodo.org/record/1283325#.Wz5VXtJKjIV">19F NMR</a> and <a href="https://zenodo.org/record/1311686#.W0il_tJKjIU">SPR assays</a> & to solve the co-crystal structures to determine if electron density of ligands can be seen in the binding pocket of the protein domain.</p>
Single Crystal X-ray Diffraction Data for PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
<p>Single Crystal X-ray Diffraction Data for PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein collected at Diamond Light Source, Beamline I03 2018-07-21</p>
How small amounts of Ge modify the formation pathways and crystallization of kesterites
<p>The inclusion of Ge into the synthesis of Cu2ZnSn(S,Se)4 absorbers for kesterite solar cells has been proven to<br> be a very efficient way to boost the device efficiency in a couple of recent publications. This highlights the<br> importance to elucidate the mechanisms by which Ge improves the kesterite solar cells properties to such a<br> large extent. In this contribution, we first show how controlling the position and thickness of a very thin<br> (10–15 nm) layer of Ge greatly influences the crystallization of kesterite thin films prepared in a sequential<br> process. Typically, Cu2ZnSnSe4 (CZTSe) films form in a bi-layer structure with large grains in the upper region<br> and small grains at the back. By introducing Ge nanolayers below our precursors, we observe that large<br> CZTSe grains extending over the whole absorber thickness are formed. Additionally, we observe that Ge<br> induces fundamental changes in the formation mechanism of the kesterite absorber. In a detailed analysis of<br> the phase evolution with and without Ge, we combine the results of X-ray fluorescence, X-ray diffraction<br> and Raman spectroscopy to demonstrate how the Ge influences the preferred reaction scheme during the<br> selenization. We reveal that the presence of Ge causes a large change in the in-depth elemental distribution,<br> induces a stabilizing Cu–Sn intermixing, and thus prevents drastic compositional fluctuations during the<br> annealing process. This finally leads to a change from a tri-molecular towards, mainly, a bi-molecular CZTSe<br> formation mechanism. Kesterite thin films with surprisingly large crystals of several microns in diameter can<br> be fabricated using this approach. The results are related to the increase in device performance, where power<br> conversion efficiencies of up to 11.8% were obtained. Finally, the consequences of the disclosed crystallization<br> pathways and the extension to other chalcogenide technologies are discussed.</p>
Diffraction images of a crystal of a SH3 domain
<p>Data were collected on a single crystal at the beamline i03 of the Diamond synchrotron facility (Didcot, UK) using radiation of 0.99998 Å wavelength and a PILATUS3 6M detector. The dataset consists of 3600 images (0.1 degree oscillation per image). Data extend to ~1.1 Å resolution.</p>
Silicon Single Crystal Diffraction Pattern
<p>Single crystal silicon pattern, as used in AstroEBSD (https://arxiv.org/abs/1804.02602).</p> <p>The pattern can be indexed with a pattern centre of [0.5, 0.18, 0.62] (PCx, PCy, PCz - using AstroEBSD conventions) and it will return Euler angles of (-47.7, 73.9, -71.9) in degrees with a ZXZ convention. This is shown in figure 9 of the AstoEBSD paper.</p>
Raw diffraction images of cypovirus polyhedra crystals containing Pd(allyl) complexes
<p>Diffraction images of wild type cypovirus polyhedra in-vivo crystals (WTPhC) and the mutant (Δ3-PhC) related to PDB codes <a href="https://www.rcsb.org/structure/5YHA">5YHA</a> and <a href="https://www.rcsb.org/structure/5YHB">5YHB</a>, respectively (<a href="http://dx.doi.org/10.1039/c7cp06651a">Abe et al., 2017, Phys. Chem. Chem. Phys.</a>).</p> <p>Small-wedge (5° or 10°/crystal) datasets were collected from loop-harvested microcrystals automatically with ZOO system using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8.</p> <p>The crystals belonged to space group I23 with unit cell parameter a~103 Å. All datasets were processed and merged using KAMO pipeline with XDS.</p> <p>NOTE that master.h5 files were modified; see <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md">https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md</a>.</p>
Raw diffraction images of cross-linked cypovirus polyhedra mutant crystals
<p>Diffraction images of cross-linked cypovirus polyhedra mutant crystals related to PDB codes <a href="https://www.rcsb.org/structure/5YR1">5YR1</a>, <a href="https://www.rcsb.org/structure/5YR9">5YR9</a>, <a href="https://www.rcsb.org/structure/5YRA">5YRA</a>, <a href="https://www.rcsb.org/structure/5YRB">5YRB</a>, <a href="https://www.rcsb.org/structure/5YRC">5YRC</a>, and <a href="https://www.rcsb.org/structure/5YRD">5YRD</a> (<a href="http://dx.doi.org/10.1039/c7cc08689j">Negishi et al. 2018, Chem. Commun.</a>).</p> <p>Small-wedge (5° or 10°/crystal) datasets were collected from loop-harvested microcrystals at a wavelength of 1 Å on BL32XU and BL41XU, SPring-8. The datasets for 5YR1, 5YR9, 5YRB, and 5YRC were collected automatically using ZOO system.</p> <p>The crystals belonged to space group I23 with unit cell parameter a~103 Å. All datasets were processed and merged using KAMO pipeline with XDS.</p> <p>This entry includes following data:</p> <ul> <li> <p>1-PhC (5YR1, 1.72 Å)</p> <ul> <li> <p>BL32XU (EIGER X 9M)</p> </li> <li> <p>5°/crystal ×32 (0.1°/frame)</p> </li> </ul> </li> <li> <p>2-PhC (5YR9, 1.70 Å)</p> <ul> <li> <p>BL32XU (MX-225HS)</p> </li> <li> <p>5°/crystal × 127 (1°/frame)</p> </li> </ul> </li> <li> <p>3-PhC (5YRA, 1.79 Å)</p> <ul> <li> <p>BL41XU (PILATUS3 6M)</p> </li> <li> <p>5° or 10°/crystal × 49 (0.25°/frame)</p> </li> </ul> </li> <li> <p>ox1-PhC (5YRB, 1.65 Å)</p> <ul> <li> <p>BL32XU (EIGER X 9M)</p> </li> <li> <p>5°/crystal × 78 (0.1°/frame)</p> </li> </ul> </li> <li> <p>ox2-PhC (5YRC, 1.67 Å)</p> <ul> <li> <p>BL32XU (MX-225HS)</p> </li> <li> <p>5°/crystal × 323 (1°/frame)</p> </li> </ul> </li> <li> <p>ox3-PhC (5YRD, 1.85 Å)</p> <ul> <li> <p>BL41XU (PILATUS3 6M)</p> </li> <li> <p>5°/crystal × 29 (0.25°/frame)</p> </li> </ul> </li> </ul> <p>NOTE that EIGER's master.h5 files were modified; see <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md">https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md</a>.</p>
Supplementary materials for the paper "Computing with liquid crystal fingers: Models of geometric and logical computation." Physical Review E 84.6 (2011): 061702.
<p>When a voltage is applied across a thin layer of cholesteric liquid crystal, fingers of cholesteric alignment can form and propagate in the layer. In computer simulation, based on experimental laboratory results, we demonstrate that these cholesteric fingers can solve selected problems of computational geometry, logic, and arithmetics. We show that branching fingers approximate a planar Voronoi diagram, and nonbranching fingers produce a convex subdivision of concave polygons. We also provide a detailed blueprint and simulation of a one-bit half-adder functioning on the principles of collision-based computing, where the implementation is via collision of liquid crystal fingers with obstacles and other fingers.</p>
Raw Data from Fluoroacetate Dehalogenase Solved by Serial Oscillation Crystallography (1° oscillation per crystal), PDB 6MUH
<p>This is the raw data for PDB 6MUH: Fluoroacetate dehalogenase, room temperature structure solved by serial 1 degree oscillation crystallography.</p> <p>Data was taken at Beamline G3 of CHESS at 10.2 keV (1.2155 Å). Collection date was 2018-03-04. Beam size 7 µm V x 9 µm H, flux 2e11 ph/s. Detector: Dectris EIGER X 1M. Data format: Dectris HDF5 for EIGER. Rotation was counterclockwise about the laboratory Z-axis ( 0 -1 0 in the XDS coordinate system). Detector distance was 45 mm.</p> <p>One degree from each data well was collected, at 0.2° per frame. Each well has five data frames. Data was collected in four successive iterations, labeled 000-003, of 1600 wells; each *master.h5 corresponds to 8000 data frames. </p>
Single crystal diffraction raw data for Fampridine hydrochloride Phase 3
<p>A set of diffraction images (in both Denzo .x and Bruker Nonius .kcd formats) collected on a Bruker Nonius KappaCCD diffractometer on an FR591 rotating anode generator equipped with confocal mirrors.</p> <p>The sample is Phase 3 of the Fampridine hydrochloride organic salt - a system that forms numerous complicated phases. The authors wish to make the raw data available so that those who wish to explore the modelling of these exceptionally complex systems may process the data themselves.</p>
Single crystal diffraction raw data for Fampridine hydrochloride Phase 4
<p>A set of diffraction images in Rigaku Oxford Diffraction (img) format, collected on a Rigaku FRE+ diffractometer, equipped with HF Varimax confocal mirrors and an AFC12 goniometer and HG Saturn 724+ detector diffractometer.</p> <p>The sample is Phase 4 of the Fampridine hydrochloride organic salt - a system that forms numerous complicated phases. The authors wish to make the raw data available so that those who wish to explore the modelling of these exceptionally complex systems may process the data themselves.</p>
Single crystal diffraction raw data for Fampridine hydrochloride Phase 1
<p>A set of diffraction images (in both Denzo .x and Bruker Nonius .kcd formats) collected on a Bruker Nonius KappaCCD diffractometer on an FR591 rotating anode generator equipped with confocal mirrors.</p> <p>The sample is Phase 1 of the Fampridine hydrochloride organic salt - a system that forms numerous complicated phases. The authors wish to make the raw data available so that those who wish to explore the modelling of these exceptionally complex systems may process the data themselves.</p>
Raw and processed anomalous diffraction data for crystals of metal-free R2lox soaked with Mn, Fe and Co or Zn
<p>Raw and processed anomalous diffraction data for crystals of metal-free <em>Geobacillus kaustophilus</em> R2-like ligand-binding oxidase (R2lox) soaked with 5 mM each MnCl<sub>2</sub>, (NH<sub>4</sub>)<sub>2</sub>Fe(SO<sub>4</sub>)<sub>2</sub> and CoCl<sub>2</sub> or ZnCl<sub>2</sub>. Data were collected on two crystals each after soaking with Mn, Fe and Co or Mn, Fe and Zn, respectively. For each crystal, one dataset each was collected at the Fe K edge (7162 eV), Mn K edge (6589 eV) and Co K edge (7721 eV) or Zn K edge (9664 eV; X-ray energies corresponding to the theoretical K edge + 50 eV). Data were collected at 100 K on a Pilatus 6M detector at beamline X06SA of the Swiss Light Source (SLS, Villigen, Switzerland) on September 23, 2012, and processed with XDS and XSCALE. All raw and processed diffraction data for each crystal are compressed into one file. </p>
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