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opencc-by-4.0Apr 2019View details →

Raw diffraction images of prokaryotic peptide transporter PepTSo2

Diffraction images of prokaryotic peptide transporter PepTSo2. In Nagamura et al. (<a href="https://doi.org/10.1107/S2053230X19003546">Acta Cryst. F, 2019</a>), the crystal form A (PDB code: <a href="http://www.rcsb.org/structure/6JKD">6JKD</a>, space group I4, 3.9 Å resolution) and the form B (PDB code: <a href="http://www.rcsb.org/structure/6JKC">6JKC</a>, space group P4212, 3.5 Å resolution) were reported. Small-wedge (5 or 10°/crystal) datasets collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. PepT-So2_171220_BL32XU_{1..4}.tar.xz contains directories 01, 07-1, 07-2, 09, 10, 11. PepT-So2_180215_BL32XU.tar.xz contains directories 01, 02, 03, 04, 05, 14. Different directories are from different crystallization conditions. It seems they have different space groups even though they may share the same reduced cells. In the literature for form A data (I4, a=b=115, c=110 Å) from 07-2 and 11 of 171220_BL32XU were used while for form B data (P4212, a=b=119, c=104.3 Å) from 04 and 05 of 180215_BL32XU were used. 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>.

opencc-by-4.0Jun 2019View details →

Raw diffraction images of human ETB receptor in complex with IRL2500

Crystal structure of the thermostabilized human ETB receptor in complex with peptide inverse agonist IRL2500 (PDB code: <a href="https://www.rcsb.org/structure/6K1Q">6K1Q</a>). Small-wedge (5-10°/crystal) datasets collected from loop-harvested microcrystals using <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md">EIGER</a> X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. Beam size was around 10×10 µm2 and oscillation step was 0.1°. The crystals belonged to space group I422 with unit cell parameters a=b~110, c~292 Å. In total 441 datasets were collected, and of these 428 datasets were indexed and integrated using XDS with <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline. 88 integrated results were manually selected and finally 58 were merged at 2.6 Å resolution after CC-based clustering and outlier rejection by KAMO in the published result (<a href="https://doi.org/10.1038/s42003-019-0482-7">Nagiri et al. Communications Biology, 2019</a>).

opencc-by-4.0Apr 2024View details →

BIR-MicroED: TEM image series revealing bend contour motion in static microcrystals (biotin, Zn(II)-methionine, Co(II)-porphyrin, AVAAGA) and diffraction patterns acquired from the same crystals at 200 kV

This deposition contains a series zip files each containing TEM image series and electron diffraction images in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). Zip files are named according to the format: "CompoundName_bendcontour_imageseries_AcceleratingVoltage_Temperature.zip" Data is further divided into sub-directories according to the particular crystal studied (crystal1, crystal2, crystal3), each containing a TEM image series (name format: "CompoundName_static_imageseries_AcceleratingVoltage_Temperature_crystal#.mrc") and 10 diffraction snapshots (2 frames each, each convering 1 second of electron beam exposure) acquired at equally spaced time intervals throughout the image series. These are named according to the format: "CompoundName_bendcontour_crystal#_diffraction_snap#.mrc"

opencc-by-4.0Nov 2018View details →

Raw diffraction images of the type VI amidase immunity (Tai4) and the effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens

X-ray diffraction images of the type VI amidase immunity (Tai4) and the effector-immunity complex (Tae4-Tai4) crystals from Agrobacterium tumefaciens. This upload includes: <ul> <li>AtTai4 (PDB code: 6IJE) collected on BL41XU, SPring-8 using PILATUS3 6M detector. <ul> <li>0.5°/frame × 360 frames (helical data collection)</li> <li>P212121, a=53.92, b=57.76, c=71.47 Å</li> </ul> </li> <li>AtTae4-AtTai4 complex (PDB code: 6IJF) collected on BL32XU, SPring-8 using MX225-HS CCD detector. <ul> <li>0.5°/frame × 360 frames (helical data collection)</li> <li>P61, a=b=72.03, c=194.35 Å</li> </ul> </li> </ul>

opencc-by-4.0Nov 2022View details →

Electron backscatter diffraction data and backscatter electron images from four conditions from a cold-rolled and annealed Al-Mn alloy

Raw electron backscatter diffraction (EBSD) datasets and backscatter electron (BSE) images acquired from four conditions from a cold-rolled and non-isothermally annealed Al-Mn alloy: as deformed, 175 C, 300 C and 325 C. The heating rate is 50 C/h. The material is recovered after 300 C and partly recrystallized after 325 C. The data forms part of the supplementary material to the paper "Orientation dependent pinning of (sub)grains by dispersoids during recovery and recrystallization in an Al-Mn alloy" (2023) published in Acta Materialia (https://doi.org/10.1016/j.actamat.2023.118761). The data was acquired in order to study the effect of particles on recovery and recrystallization in the Al-Mn alloy. The particles detected in the BSE images were inserted in the EBSD map after the EBSD map had been corrected for distortions by image registration using the BSE images. See the GitHub repository https://github.com/hakonanes/p-texture-al-mn-alloys for Jupyter notebooks and MTEX (MATLAB) and ImageJ scripts used to process and analyze the data. See the README.txt file for a description of the file contents.

opencc-by-4.0Jun 2023View details →

Datesets and images of the publication "Probing crystallinity and grain structure of 2D materials and 2D-like van der Waals heterostructures by low-voltage electron diffraction" - DOI: 10.1002/pssa.202300148

Datasets and images of the publication "Probing crystallinity and grain structure of 2D materials and 2D-like van der Waals heterostructures by low-voltage electron diffraction" - DOI: <a href="https://www.doi.org/10.1002/pssa.202300148">10.1002/pssa.202300148</a> The Jupyter Notebooks for analyzing the datasets and generating all the figures are available at <a href="https://gitlab.com/JohMu/tds_hios_manuscript">https://gitlab.com/JohMu/tds_hios_manuscript</a>. MoS2 4D-STEM dataset: <ul> <li>192x192 scan pixels</li> <li>200x200 camera pixels</li> <li>Acceleration voltage: 20kV</li> <li>Camera length: 10.56 mm</li> <li>Camera pixel size: 4x5.86 µm = 23.44 µm (original dataset with 4x4 binning)</li> <li>File location: Figure 2_3_S1.zip -> 230101205338_20kV_hexz0_camz-10_posi_003_good\scan_data_bin2_centered_crop-imgNx200.h5</li> <li>The original raw dataset (23 GB, 192x192 scan pixels, 800x800 camera pixels, camera pixel size: 5.86 µm), the scan reference dataset and the Jupyter Notebook for the shift-compensation is available from the author. The dataset uploaded here is binned by a factor of 4 and shift-compensated.</li> </ul> C60/MoS2 4D-STEM dataset: <ul> <li>113x113 scan pixels</li> <li>512x512 camera pixels</li> <li>Acceleration voltage: 20kV</li> <li>Camera length: 20.56 mm</li> <li>Camera pixel size: 5.86 µm</li> <li>File location: Figure 4.zip -> scan_data_scan113x113_gzip.h5</li> </ul>

opencc-by-4.0Oct 2023View details →

Raw diffraction images of [NiFe]-hydrogenase maturation factor HypD from Aquifex aeolicus (C360S mutant)

HypD is one of the maturation factors of [NiFe]-hydrogenase and can form a complex with other maturation factors (Muraki et al., 2019).  We used datasets to investigate the protocol of detecting polymorphs using Hierarchical clustering (Acta D., submitted). All diffraction datasets were collected at BL45XU, SPring-8, using an automated data collection system ZOO. From six crystals, datasets were collected from each one using a continuous helical scan scheme for 360º oscillation with the following experimental parameters; Beam size: 20 µm × 20 µm, Wavelength: 1.0000 Å, Total dose/crystal: 10 MGy, Detector: EIGER X 9M (DECTRIS Co. Ltd.). All crystals belonged to space group P212121 with unit cell parameters roughly corresponding to a=60.0, b=62.6, c=97.6 Å.

opencc-by-4.0Oct 2023View details →

Raw diffraction images of 5-Chlorotryptamine-bound trypsin

Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting these long chains of amino acids into smaller pieces.  We used datasets to investigate the protocol of detecting polymorphs using Hierarchical clustering (Acta D., submitted). All diffraction data were collected at BL32XU, SPring-8, using an automated data collection system ZOO. Data were acquired from four crystals of 5-Chlorotryptamine-bound trypsin. All datasets were collected using a continuous helical scan scheme for 360º oscillation with the following experimental parameters; Beam size: 10 µm × 15 µm, Wavelength: 1.0000 Å, Total dose/crystal: 10 MGy, Detector: EIGER X 9M (DECTRIS Co. Ltd.). All crystals belonged to space group P212121 with unit cell parameters roughly corresponding to a=54.5, b=58.6, c=66.6 Å.

opencc-by-4.0Oct 2023View details →

Raw diffraction images of 4-Methoxybenzamidine-bound trypsin

Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting these long chains of amino acids into smaller pieces.  We used datasets to investigate the protocol of detecting polymorphs using Hierarchical clustering (Acta D., submitted). All diffraction data were collected at BL32XU, SPring-8, using an automated data collection system ZOO. Data were acquired from four crystals of 4-Methoxybenzamidine -bound trypsin. All datasets were collected using a continuous helical scan scheme for 360º oscillation with the following experimental parameters; Beam size: 10 µm × 15 µm, Wavelength: 1.0000 Å, Total dose/crystal: 10 MGy, Detector: EIGER X 9M (DECTRIS Co. Ltd.). All crystals belonged to space group P212121 with unit cell parameters roughly corresponding to a=54.6, b=58.6, c=66.7 Å.

opencc-by-4.0Aug 2019View details →

Raw Diffraction Images: Formation of a highly dense tetra rhenium cluster in a protein crystal and its implications in medical imaging.

Exploration of a “time on shelf” protein structure containing the radiopharmaceutical synthon fac-[Re(CO)3(H2O)3]+ as an in vivo reaction vessel to form tetranuclear rhenium clusters appropriate for theranostic applications.That a protein crystal can serve as a chemical reaction vessel is intrinsically fascinating. That it can produce an electron dense tetranuclear rhenium cluster compound from a rhenium tricarbonyl tribromo starting compound adds to the fascination. The cluster has been synthesised before in vitro when it formed under basic conditions. Therefore its synthesis in a protein crystal grown at pH4.5 is even more unexpected. The X-ray crystal structures presented here are for the protein hen egg white lysozyme incubated with the rhenium tricarbonyl tribromo compound for periods of 1 year and 2 years. These reveal a completed, very well resolved, tetra rhenium cluster after two years and an intermediate state after 1 year where the carbonyl ligands to the rhenium cluster are not yet clearly resolved. A dense tetra-nuclear rhenium cluster, and its technetium form, offers enhanced medical imaging contrast. The raw diffraction images for the one year and two year protein structure, described in the manuscript, is made avaliable on the Zenodo repository.

opencc-by-4.0Dec 2018View details →

Diffraction images for PDB entry 6TPI - Structure of EnvC bound to the periplasmic domains of FtsX

X-ray diffraction images for complex collected at Diamond Light Source in the UK.

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

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-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.