Find research datasets worth reusing

opencc-by-sa-4.0Jun 2017View details →

Diffraction images of a crystal of the spectrin repeats 7, 8, and 9 (SR7-SR9) of the plakin domain of human plectin (PDB code 5J1I)

Diffraction images of crystals of a fragment of the plakin domain of human plectin that includes the spectrin repeats 7 to 9 (SR7-SR9). Images correspond to the dataset used to solve and refine the pdb entry 5J1I (http://www.rcsb.org/pdb/explore/explore.do?structureId=5J1I). Data were collected on a single crystal at the beamline 14.2 of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using radiation of 0.9330 Å wavelength and an ADSC Q4 CCD detector. The dataset consists of 360 images (1 degree oscillation per image). Diffraction data is highly anisotropic. Based on analysis with the STARANISO server (http://staraniso.globalphasing.org/) data extend approximately to 5.0, 3.8, and 2.6 Å resolution along the three principal directions of anisotropy, which are 0.555 a*+ 0.832 c*, b*, and -0.361 a* + 0.932 c*, respectively.

opencc-by-sa-4.0Jun 2017View details →

Diffraction images of crystals of the spectrin repeats 7 and 8 (SR7-SR8) of the plakin domain of human plectin (PDB code 5J1G): native and Hg-derivative datasets for phasing by SIRAS

Diffraction images of crystals of a fragment of the plakin domain of human plectin that includes the spectrin repeats 7 to 8 (SR7-SR8). Images correspond to the dataset used to solve and refine the pdb entry 5J1G (http://www.rcsb.org/pdb/explore/explore.do?structureId=5J1G). The structure was phase by single isomorphous replacement with anomalous scattering (SIRAS) using two datasets: one from a native crystal and another one from a crystal derivatized with the mercurial compound ethylmercurithiosalicylate (EMTS). The Native dataset was collected on a single crystal at the beamline XALOC of the ALBA Synchrotron (Barcelona, Spain) using radiation of 0.9792 Å wavelength and a PILATUS 6M detector. The dataset consists of 4 wedges of 450 images each (0.2º oscillation per image). Each wedge was collected at a different position of the same crystal. The crystals belong to the space group P21 with approximate cell dimensions a=45.7 Å, b=115.9 Å, c=64.8 Å, beta=97.6 º. The data from a mercurial derivative (EMTS) was collected in house using a rotating anode X-ray generator (wavelength 1.54179 Å) and a mar345 image plate detector. The dataset consists of 360 images (1º oscillation per image). The crystal was isomorphic to the native crystal. In addition to the diffraction images the following files are included: a) Files for indexing with the program XDS and the HKL files containing the integrated intensities. b) Files for scaling using the program xscale (directory XSCALE_5J1G_Native_EMTS). c) The directory “phasing_shelx” contains hkl files of the intensities of the native and EMTS datasets in a format suitable for analysis with Shelx. This directory also contains the files of the phasing by SIRAS using Shelx C/D/E.

opencc-by-4.0Apr 2024View details →

Alpha-Galactosaminidase family GH191 protein from Environmental sample (99.2% identity to Myxococcus fulvus enzyme): X-ray diffraction images

This submission includes a zip archive of diffraction images recorded with the Dectris EIGER X 9M detector at the DIAMOND beamline I04-1. The model of the crystal structure and associated information can be found in the Protein Data Bank entry 9EP5. This is a case of crystal pathology – partial disorder. The model has C 2 2 21 symmetry and two molecules per asymmetric unit with occupancies 1 and 1/3. The molecule with partial occupancy overlaps with a symmetry related molecule.

opencc-by-4.0Mar 2019View details →

RefleX: X-ray diffraction images dataset

Image dataset prepared for the RefleX study, described in "Detecting anomalies in X-ray diffraction images using Convolutional Neural Networks". The dataset contains 6311 X-ray diffraction images in 1024x1024 png format (reflex_img_1024_inter_nearest.zip). The repository also contains a file mapping each image to a set of labels (labels.csv) and files describing the assignment of each image to training, validation, and testing sets (labels_train.csv, labels_val.csv, labels_test.csv). The dataset can be used for multi-label classification. Each diffraction image can exhibit any combination of seven classes: Ice ring, Diffuse Scattering, Background Ring, Non-uniform Detector, Loop Scattering, Strong Background, and Artifact.

opencc-by-4.0Jun 2019View details →

X-ray diffraction images of Anti-CD20 crystals

Original X-ray diffraction images from Pilatus detector taken at Diamond Light Source Synchrotron (I04 beamline). Images can be read by AXDV (or similar) software. These datasets were used for diffraction and crystallographic analyses reported in Yang et al., Crystals 2019, 9, 230.

opencc-by-4.0Nov 2022View details →

Raw Data: Gold Coated ZnO Microstructures by Bragg Coherent X-Ray Diffraction Imaging

Two sets of raw data from gold coated ZnO microstructure (rod) investigated by Bragg coherent X-ray diffraction imaging used in publication: "Visualizing Intrinsic 3D-Strain Distribution in Gold Coated ZnO Microstructures by Bragg Coherent X-Ray Diffraction Imaging and Transmission Electron Microscopy with Respect to Piezotronic Applications" (<a href="https://doi.org/10.1002/aelm.202100546">https://doi.org/10.1002/aelm.202100546</a>) Included is data from two different spatial positions along the c-axis of the ZnO rod. Futher on called position 1 (P1) and position 2 (P2). For each position there is a .nxs file of a rocking scan around the {10-10} Bragg reflection, collected by a 2D detector and other recorded values, e.g. motor positions, counter values.

opencc-by-4.0Jan 2020View details →

Raw diffraction images of the first bromodomain of human BRD4 in complex with (+)-JD1

Raw diffraction images of the first bromodomain of human BRD4 in complex with (+)-JD1, an Organometallic BET Bromodomain Inhibitor. The final structure is deposited in the Protein Data Bank under accession code <a href="http://www.rcsb.org/structure/6SE4">6SE4</a>. The structure is part of the following publication: Hassell-Hart, S., Runcie, A., Krojer, T., Doyle, J., Lineham, E., Ocasio, C.A., Neto, B.A.D., Fedorov, O., Marsh, G., Maple, H., et al. (2019). Synthesis and Biological Investigation of (+)-JD1, an Organometallic BET Bromodomain Inhibitor. Organometallics. doi: 10.1021/acs.organomet.9b00750.   Additional information: dataset: BRD4A-JD1_i03 beamline: Diamond Light Source I03 visit:  mx19301-7 date: 25-11-2018 Flux: 2.03e+11 Ω Start: 0.0° Ω Osc: 0.15° Ω Overlap: 0° No. Images: 1200 Resolution: 1.50Å Wavelength: 0.9762Å Exposure: 0.030s Transmission: 100.00% Beamsize: 80x20μm datasets: BRD4A-JD1_i04 beamline: Diamond Light Source I04 visit:  mx19301-9 date: 08-12-2018 Flux: 6.62e+11 Ω Start: 0.0° Ω Osc: 0.50° Ω Overlap: 0° No. Images: 720 Resolution: 2.30Å Wavelength: 1.7384Å Exposure: 0.050s Transmission: 100.00% Beamsize: 32x20μm Additionally, a cif file containing refinement restraints and a png file for the ligand JD1 is included.

opencc-by-4.0Jan 2020View details →

Raw diffraction images of endothelin ETB receptor in complex with sarafotoxin S6b

Diffraction images of endothelin ETB receptor in complex with sarafotoxin S6b (PDB code: <a href="https://www.rcsb.org/structure/6LRY">6LRY</a>). 4 datasets were collected with helical method (60-120°/crystal), and 28 small-wedge (10°/crystal) datasets were collected manually. The diffraction images were collected from loop-harvested microcrystals using an <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. 16 datasets were merged at 3.0 Å resolution in the published result (<a href="https://doi.org/10.1016/j.bbrc.2019.12.091">Izume et al. BBRC 2020</a>) using XDS with <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline. NOTE <ul> <li>Most frames have (relatively weak) lipid rings.</li> </ul>

opencc-by-4.0Feb 2020View details →

Raw diffraction images of Drosophila Piwi

Crystal structure of Drosophila Piwi (PDB code: <a href="https://www.rcsb.org/structure/6KR6">6KR6</a>). 28 mercury-bound data and 4 native data were included (see file_list.txt for details). Each dataset consists of 180° (except two 90° datasets) from single crystal and was collected 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 with helical data collection scheme using 15×10 μm beam on BL32XU, SPring-8.  All diffraction images were processed using DIALS 1.10.2 through <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline, and merged using XSCALE from XDS package with kamo.multi_merge. The crystals belong to space group P212121 with a=62.1, b=115.6, c=119.9 Å. Finally 23 mercury-bound datasets were merged at 2.9 Å resolution in the published result (<a href="https://doi.org/10.1038/s41467-020-14687-1">Yamaguchi et al. Nature Communications, 2020</a>). Merging improved resolution and electron density of PAZ domain that was difficult to interpret with a single dataset.

opencc-by-4.0May 2020View details →

Raw diffraction images of heliorhodopsin E108D mutant

Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant (PDB code: <a href="https://www.rcsb.org/structure/7CLJ">7CLJ</a>). 79 small-wedge (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 5×5 µm2 and oscillation step was 0.1°. The crystals belonged to space group P42212 with unit cell parameters a~72.9, c~115 Å. 52 datasets were indexed and integrated using XDS with <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline. Finally 12 integrated results 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/10.1016/j.bbrc.2020.06.124">Tanaka et al. BBRC, 2020</a>).

opencc-by-4.0Nov 2020View details →

Raw diffraction images of linker-PDE and TMD-linker of RhPDE

Crystal structures of linker-PDE (PDB code: 7D7P) and TMD-linker (PDB code: 7D7Q) of Rhodopsin phosphodiesterase (Rh-PDE). For TMD (PDB code: 7CJ3) please refer to <a href="https://cxidb.org/id-171.html">CXIDB ID 171</a>. TMD-linker: 91 small-wedge (10 or 5°/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 15×10 or 5×5 µm2 and oscillation step was 0.1°. The crystals belonged to space group I222 with unit cell parameters a~76, b~137, c~207 Å.  74 datasets were indexed and integrated using XDS with <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline. Finally 58 integrated results were merged at 3.5 Å resolution after CC-based clustering and outlier rejection by KAMO in the published result. Linker-PDE: 128 small-wedge (10°/crystal) datasets collected from different potions of a few large crystals broken in cryoloops 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 15×10 µm2 and oscillation step was 0.1°. The crystals belonged to space group C2 with unit cell parameters a~117, b~68, c~57 Å, β~111°. 109 datasets were indexed and integrated using XDS with <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline. Finally 64 integrated results were merged at 2.1 Å resolution after CC-based clustering and outlier rejection by KAMO in the published result.

opencc-by-4.0Sep 2016View details →

MAD diffraction images for yeast 5-aminolevulinic acid dehydratase (ALAD).

Selenomethionine multiwavelength anomalous dispersion (MAD) diffraction images for the original structure determination of 5-aminolevulinic acid dehydratase (ALAD) from yeast collected at the bending magnet beamline BM14, ESRF, Grenoble (25-27 Sept 1996). There are separate folders for the data from different wavelengths (l1 is the edge dataset, l4 is the edge inverse beam, l2 is the peak, l5 and l55 are the peak inverse beam (l55 is an overlapping continuation of l5 due to beam loss), l3 is the remote and l6 is the remote inverse beam). The seoa folder contains the selenium 'optimised anomalous' peak data. The images were collected with a Mar Research image plate and each folder has a file called 'mos.com' giving the data collection parameters for that run except for the exposure times which were 45 seconds per image for both l1 and l2, 55 seconds per image for the remote l3 and 120 seconds per image for the optimised anomalous collection (seoa). The latter dataset does not have a file listing the parameters which were: crystal-to-detector distance 275mm, delta-phi 1 degree, wavelength 0.9791 Angstroms, big-MAR format (note other datasets were collected in small-MAR format).

opencc-by-4.0Nov 2016View details →

X-ray diffraction images for human recombinant 5-aminolevulinic acid dehydratase (ALAD).

X-ray diffraction images for recominant human 5-aminolevulinic acid dehydratase (ALAD) collected at ESRF (Grenoble) beam line ID14-2 using an ADSC Quantum 4 detector to a resolution of 2.8 Å. A series of 1 ̊ oscillation images were recorded with an exposure time of 10 seconds per image. More details are given with the scanned notes and the log file.

opencc-by-4.0Nov 2016View details →

X-ray diffraction images for human native 5-aminolevulinic acid dehydratase (ALAD).

X-ray diffraction images of human native ALAD collected at station 9.5 at synchrotron radiation source (SRS) Daresbury, UK, with a Marresearch 345 image plate detector on Sunday 26th April 1998. More details of the data collection are given in the files suffixed SUMMARY.

opencc-by-4.0Nov 2016View details →

Original X-ray diffraction images for 5-aminolevulinic acid dehydratase (ALAD) from E. coli complexed with porphobilinogen.

The diffraction images which allowed the original 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.

Atomic resolution X-ray diffraction images for methanol dehydrogenase from Methylobacterium extorquens.

Atomic resolution X-ray diffraction images for methanol dehydrogenase from Methylobacterium extorquens collected at ESRF (Grenoble, France) using beamline ID29 in May 2002 with an ADSC detector. The diffraction resolution for the first pass is approximately 1.1 - 1.2 Angstroms and a second pass was collected to recoup the reflections that were overloaded in the first pass. More details of the data collection are in the included scanned notes and log files.

X-ray diffraction images for cytochrome cL from the methylotrophic bacterium Methylobacterium extorquens.

X-ray diffraction images for cytochrome cL from Methylobacterium extorquens collected at the ESRF beamline ID14-2 using an ADSC detector in Feb 2001. The diffraction data extend to around 2.0 Angstroms resolution and were used for the initial structure determination of this protein. Further details in the log files and the notes.

Atomic resolution X-ray diffraction images of native endothiapepsin.

X-ray diffraction images that were collected at DESY (Hamburg) to a resolution of 0.9 Angstroms from native endothiapepsin. The data were collected using a MAR345 detector at beamline BW7B in June 1999. More details are in the included notes.

Atomic resolution X-ray diffraction images for endothiapepsin complexed with the inhibitor H261.

X-ray diffraction images for a complex of endothiapepsin with the hydroxyethylene renin inhibitor H261 which were collected at DESY (Hamburg) in June 1998 using the beamline BW7B with a Mar image plate detector in two passes. The data extend to a resolution of almost 1.1 Angstroms. More details are given in the accompanying notes.

X-ray diffraction images for 5-aminolevulinic acid dehydratase with a putative reaction intermediate resembling the product porphobilinogen bound.

X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase co-crystallised with the substrate 5-aminolevulinic acid. The structure demonstrated a putative product-like intermediate bound covalently to Lys 263 with an amino side chain ligated to the active-site zinc ion in a position normally occupied by a catalytic hydroxide ion. The data were collected in two passes using the ESRF beamline ID29 in Feb 2002 and extend to approximately 1.6 Å resolution.