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opencc-by-4.0Jan 2020View details →

USP5 ZnF-UBD Co-Crystal Structure with Compound UBTR012574a

Objective: To grow well-diffracting co-crystals of USP5 zinc finger ubiquitin binding domain (ZnF-UBD) to solve the co-crystal structures to determine ligand interactions in the binding pocket and to determine if the predicted binding pose is similar to the experimental binding pose.

opencc-by-4.0Oct 2020View details →

X-ray computed tomography of bedded halite and halite crystals from the Bonneville Salt Flats

X-ray computed tomography of bedded halite and halite crystals from the Bonneville Salt Flats, Utah.

opencc-by-4.0Jan 2017View details →

Raw diffraction images of polyhedra in-vivo crystals

Diffraction images of wild type cypovirus polyhedra in-vivo crystals (WTPhC) and the mutant (Δ3-PhC) related to PDB codes 5GQM and 5GQN, respectively. Small-wedge (5°/crystal) datasets were collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. The datasets for 5GQN were collected automatically using ZOO system. The crystals belonged to space group I23 with unit cell parameter a~103 Å. 14 and 41 datasets were merged at 1.68 and 1.55 Å resolution in the published result (Abe et al. ACS Nano 2017; PDB codes: 5GQM & 5GQN, respectively) using KAMO; see https://github.com/keitaroyam/yamtbx/wiki/Processing-Polyhedra-data-(5GQM-&-5GQN) NOTE <ul> <li> flatfield correction was not applied to the images and you need to apply it using the correction table saved in master.h5 files. </li> <li> master.h5 files were modified; see https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md </li> <li> Most frames have ice (rings). </li> </ul>

opencc-by-4.0Jul 2024View details →

Energy and specific heat for J=7/2 magnetic crystals

Complementary data for the manuscript "Specific heat of Gd3+  and Eu2+ -based magnetic compounds" by D.J. Garcia, J. Sereni and A.A. Aligia[1]. We include the energy and specific heat for many magnetic lattices. The magnetic moment is S=7/2. Interactions are taken as Heisenberg-like H = Sum_{i,\delta}  J_\delta S_i S_{i+\delta} and \delta is taken to consider first, second, and possibly more nearest neighbors. Interactions are either all FM or AF to keep the system non-frustrated. We take all |J_\delta|=1K unless otherwise stated. Computations are performed using quantum Monte Carlo (QMC) simulations from the ALPS libraries (“dirloop_sse” package) [2, 3]. Most calculations are done using 20^3 conventional unit cells. Directory name convention is as follows: fig*data/{Lattice Name}( {effective z}) , J_2 = ... , J_3 =... , K=... , L={size of the linear length} ) fig*data refers to data of the corresponding figure in reference [1]. Lattice names are BCC, Diamond, FCC, HCP, and SC  with their classic meaning of Body-Centered Cubic, Face-centered cubic, Hexagonal close-packed, and simple cubic. LHc corresponds to a layered honeycomb lattice with three NN within the plane of the honeycomb layer and one above or below the layer in alternating sites. magnetic order is either ferromagnetic (FM) or antiferromagnetic (AF). effective z agrees with the number of neighbors when all J_\delta are equal. It is computed by increasing the considered neighbor radius.  See [1]. The file SpecificHeatAndEnergy.tgz contains the raw data for all lattices in txt format. This version updates results with larger statistics. An ALPS example directory is also included. Finite size effects are almost negligible in these cases except for the antiferromagnetic simple cubic lattice ( SC_AF(6) ).   [1] D. J. Garcia, J. G. Sereni, A. A. Aligia, "Specific heat of Gd3+ and Eu2+-based magnetic compounds", arXiv:2410.23519 [2] A. Albuquerque, F. Alet, P. Corboz, P. Dayal, A. Feiguin, S. Fuchs, L. Gamper, E. Gull, S. Gürtler, A. Honecker, R. Igarashi, M. Körner et al., The ALPS project release 1.3: Open- source software for strongly correlated systems, Journal of Magnetism and Magnetic Materials 310(2, Part 2), 1187 (2007), doi:https://doi.org/10.1016/j.jmmm.2006.10.304, Proceedings of the 17th International Conference on Magnetism.  [3] B. Bauer, L. D. Carr, H. G. Evertz, A. Feiguin, J. Freire, S. Fuchs, L. Gamper, J. Gukelberger, E. Gull, S. Guertler, A. Hehn, R. Igarashi et al., The ALPS project release 2.0: open source software for strongly correlated systems, Journal of Statistical Mechanics: Theory and Experiment 2011(05), P05001 (2011), doi:10.1088/1742-5468/2011/05/P05001.

opencc-by-4.0Nov 2023View details →

Multi-Crystal XRD on Cyanophage S-2L HD phosphohydrolase (DatZ) collected at room temperature with the Plate Screener

Multi-Crystal XRD on DatZ crystals collected at room temperature with the CRIBLEUR Plate Screener during 2022_Run2_Plate on 2022-03-23 from an in-situ MiTeGen plate. Sweeps of 35.636 degrees (value to be confirmed) were collected on each crystal, for a total of 19 data sets.

opencc-by-4.0Nov 2023View details →

Sideband thermometry of ion crystals

Experimental data for thermometry measurements with a linear 4-ion crystal as well as a planar 19-ion crystal.

opencc-by-4.0Dec 2023View details →

Transition between distinct hybrid skyrmion textures through their hexagonal-to-square crystal transformation in a polar magnet

The file Manuscript data files.7z contains the experimental data used for creating the figures in the manuscript entitled "Transition between distinct hybrid skyrmion textures through their hexagonal-to-square crystal transformation in a polar magnet" that appear in Nature Communications 14, 8050 (2023).Paper abstract: Magnetic skyrmions, topological vortex-like spin textures, garner significant interest due to their unique properties and potential applications in nanotechnology. While they typically form a hexagonal crystal with distinct internal magnetisation textures known as Bloch- or Néel-type, recent theories suggest the possibility for direct transitions between skyrmion crystals of different lattice structures and internal textures. To date however, experimental evidence for these potentially useful phenomena have remained scarce. Here, we discover the polar tetragonal magnet EuNiGe3 to host two hybrid skyrmion phases, each with distinct internal textures characterised by anisotropic combinations of Bloch- and Néel-type windings.  Variation of the magnetic field drives a direct transition between the two phases, with the modification of the hybrid texture concomitant with a hexagonal-to-square skyrmion crystal transformation. We explain these observations with a theory that includes the key ingredients of momentum-resolved Ruderman–Kittel–Kasuya–Yosida and Dzyaloshinskii-Moriya interactions that compete at the observed low symmetry magnetic skyrmion crystal wavevectors. Our findings underscore the potential of polar magnets with rich interaction schemes as promising for discovering new topological magnetic phases.

opencc-by-4.0Jun 2024View details →

Data for "Mechanically-Sensitive Fluorochromism by Molecular Domino Transformation in a Schiff Base Crystal"

The dataset contains input and output files of computational chemistry by Quantum ESPRESSO and Gaussian softwares conducted on two polymorphic crystal structures of 4-nitro-N-salicylideneaniline.

Elucidating the Polymorphism of Xanthone: A Crystallization and Characterization Study

Dataset related to the publication: "Elucidating the Polymorphism of Xanthone: A Crystallization and Characterization Study". Accepted in Crystal Growth and Design on February 9th, 2024. Abstract: The aim of this work is to shed light on the polymorphism of xanthones, a class of oxygenated molecules well known for their bioactivity, including antioxidant, anticancer, and anti-inflammatory effects. Understanding the polymorphism of xanthones can enable the design of novel solid products for pharmaceutical, nutraceutical, and agrochemical applications. Prior to this work, two entries accounting for different space groups were deposited for 9-xanthone in the Cambridge Structure Database (CSD): an orthorhombic P212121 and a monoclinic P21 structure solved at room and low temperatures, respectively. However, the very high similarity between these two structures and the lack of clear differences in the physical properties (e.g., thermal behavior) suggested the possibility of the existence of only one crystal structure. In fact, the differences shown in the literature data might be related to the chosen operating parameters, as well as the instrumental resolution of the single-crystal X-ray diffraction experiments. In the work presented here, the ambiguity in the polymorphism of xanthone is investigated using thermal analysis, powder and synchrotron single-crystal XRD, and optical microscopy. Additionally, a workflow for the correct identification of twinned crystal structures, which can be applied to other polymorphic systems, is presented. Such workflow combines the collection of a large data set of high-resolution diffraction patterns using synchrotron radiation with the use of principal component analysis, a dimensionality reduction technique, for a quick and effective identification of phase transitions happening during the data collection. Crystallization experiments were designed to promote the formation of different crystal structures of xanthone that were recrystallized based on past literature and beyond.

STO crystal supported Pt nanodot arrays

<div> <div>Scanning Electron Microscopy (SEM) imaging of STO crystal supported Pt nanodot arrays performed with the high-resolution field-emission ThermoFisher FEI Nova Nano SEM 450 instrument operated at 2 kV using the through-lens detector (TLD) in secondary electron imaging mode.</div> <div> </div> </div>

Exponential approximation of the coherence contribution to the thermal conductivity of complex clathrate-type crystals

The low-temperature properties of guest-host crystals, such as clathrates and skutterudites, offer a rich playground for discovering novel physical phenomena and developing new materials with unique properties. The temperature dependence of thermal conductivity in these materials can exhibit both crystal-like and glass-like behavior, which reflects the properties of the phonon excitations and various scattering mechanisms. The ultra-low thermal conductivity of clathrate crystals is closely related to the concept of minimal thermal conductivity, which is determined by the intrinsic phonon scattering in the material. In this work, the temperature dependence of thermal conductivity for both crystal-like and glass-like behavior of different structural types of clathrates and skutterudites was analyzed using the ”Unified theory of thermal transport in crystals and glasses” of M. Simoncelli, N. Marzari & F. Mauri. A method was proposed and tested for the coherence contribution related to wave-like tunneling and loss of coherence between different vibrational eigenstates. The temperature dependence of the coherence contribution to thermal conductivity was approximated by the exponential function of an Arrhenius type with characteristic energy E and characteristic minimal thermal conductivity parameter κ0. The coherence contribution is intertwined with other phonon scattering mechanisms, and over a wide temperature range, its temperature dependence is universal with parameters depending on the crystal structure, positional disorder, and impurity doping. This work provides insights into the temperature dependence of thermal conductivity in guest-host materials and its importance for designing and optimizing their properties for various applications, such as thermoelectric generators

Radiation-induced point defects in KBr: CRYSTAL calculations

Calculation results on vibrational properties of radiation-induced point defects in potassium bromide, calculated using CRYSTAL17 software.

Raw diffraction images of the crystal structure of human VISTA extra cellular domain in complex with Fab fragment of pH-selective anti-VISTA antibody

The diffraction datasets was collected at X10SA, SLS. The dataset was collected from one crystal using a rotation scheme for 222º oscillation with the following experimental parameters; Wavelength: 0.9998 Å, Detector: EIGER2 Si 16M (DECTRIS Co. Ltd.). The crystal belonged to space group C 1 2 1 with unit cell parameters a=207.66, b=39.51, c=177.98 Å, and beta=117.12°.PDB ID: 8TBQ

Dataset for Main Text and SI - Squeezing the threshold of metal-halide perovskite micro-crystal lasers grown by solution epitaxy by Shuyu Zhou et al.

All data published in  Squeezing the threshold of metal-halide perovskite micro-crystal lasers grown by solution epitaxy  by Shuyu Zhou, Viktor Rehm, Hany A. Afify, Yufei Han, Jędrzej Korczak, Andrzej Szczerbakow, Tomasz Story, Zijian Peng, Albert These, Anastasia Barabash, Andres Osvet, Christoph J. Brabec, Klaus Götz, Tobias Unruh, Felix Hilpert, Olaf Brummel, Jörg Libuda, Wolfgang Heiss are summarized in this rar file.

BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (Co(II) meso-tetraphenyl porphyrin) at 200 keV

<div> This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). For each crystal, multiple subsequent sweeps (passes) at the same incident flux covering the same angular range are given. Zip files are named according to the format: "CompoundName_multipass_RotationSpeed_FrameRate_SpotSize_tiltseries_Temperature.zip" Where spot size 11 = 0.01 electrons per square Angstrom per second incident flux, and spot size 10 = 0.03 electrons per square Angstrom per second incident flux Diffraction datasets within each folder are named according to the format: "CompoundName_tiltseries_AcceleratingVoltage_Temperature_IncidentFlux_crystal#sweep#.mrc" Where crystal1sweep1 and crystal1sweep2 indicate the first and second sweep of data acquired on the same crystal, respectively. </div>

BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (Zn(II)-histidine) at 200 keV

This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). For each crystal, multiple subsequent sweeps (passes) at the same incident flux covering the same angular range are given. Zip files are named according to the format: "CompoundName_multipass_RotationSpeed_FrameRate_SpotSize_tiltseries_Temperature.zip" Where spot size 11 = 0.01 electrons per square Angstrom per second incident flux, and spot size 10 = 0.03 electrons per square Angstrom per second incident flux Diffraction datasets within each folder are named according to the format: "CompoundName_tiltseries_AcceleratingVoltage_Temperature_IncidentFlux_crystal#sweep#.mrc" Where crystal1sweep1 and crystal1sweep2 indicate the first and second sweep of data acquired on the same crystal, respectively.

BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (biotin, Zn(II)-methionine) at 200 keV

Dataset for article "W18O49 Nanowhiskers Decorating SiO2 Nanofibers: Lessons from In Situ SEM/TEM Growth to Large Scale Synthesis and Fundamental Structural Understanding" in Crystal Growth & Design, Des. 2024, 24, 1, 378–390

Supported dataset for publication "W18O49 Nanowhiskers Decorating SiO2 Nanofibers: Lessons from In Situ SEM/TEM Growth to Large Scale Synthesis and Fundamental Structural Understanding" in Crystal Growth & Design Des. 2024, 24, 1, 378–390, https://doi.org/10.1021/acs.cgd.3c01094. The directory Data contains the figures (png, jpg), and vido (AVI) source data files for the manuscript.