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9 results for “X-ray crystallography”
Diffraction data underpinning the structure of StayGold determined by X-ray crystallography (PDB code 8BXT)
<p>Raw diffraction data underpinning the crystal structure of StayGold fluorescent protein.</p> <p>This is the raw data underpinning PDB entry 8BXT.</p>
Analysis of insulin glulisine at the molecular level by X-ray crystallography and biophysical techniques
<p>Raw diffraction images for the study:- Gillis, R.B., Solomon, H.V., Govada, L. <em>et al.</em> Analysis of insulin glulisine at the molecular level by X-ray crystallography and biophysical techniques. <em>Sci Rep</em> <strong>11, </strong>1737 (2021). https://doi.org/10.1038/s41598-021-81251-2 </p> <p>PDB code 6GV0.</p>
X-ray diffraction images recorded for Aumonier et al., (2022) Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature, IUCrJ
<p>The present repository contains diffraction images corresponding to 27 distinct datasets collected at room temperature on the ESRF beamline ID30A-3 using an Eiger X 4M detector.</p> <p>Datasets have been uploaded with their original names to maintain the metadata integrity. The two following tables match the original names with those attributed in the supplementary table S1 of Aumonier et al., IUCrJ (2022) (https://doi.org/10.1107/S2052252522009150).</p> <table> <tbody> <tr> <td> <p>Data set name on Zenodo</p> </td> <td> <p>X06_01</p> </td> <td> <p>X12_05</p> </td> <td> <p>X07_02_</p> </td> <td> <p>X06_08</p> </td> <td> <p>X14_06</p> </td> <td> <p>X13_03</p> </td> <td> <p>X08_06</p> </td> <td> <p>X11_05</p> </td> <td> <p>X13_05</p> </td> <td> <p>X06_02</p> </td> <td> <p>X11_01</p> </td> <td> <p>X08_01</p> </td> <td> <p>X14_01</p> </td> <td> <p>X13_01</p> </td> <td> <p>X06_03</p> </td> </tr> <tr> <td> <p>Data set in Aumonier et al. 2022</p> </td> <td> <p>Dark</p> </td> <td> <p>PS2</p> </td> <td> <p>PS2</p> </td> <td> <p>PS3</p> </td> <td> <p>PS4</p> </td> <td> <p>PS5</p> </td> <td> <p>PS6</p> </td> <td> <p>PS7</p> </td> <td> <p>R<sub>2”</sub></p> </td> <td> <p>R<sub>3”</sub></p> </td> <td> <p>R<sub>7”</sub></p> </td> <td> <p>R<sub>10”</sub></p> </td> <td> <p>R<sub>13”</sub></p> </td> <td> <p>R<sub>21”</sub></p> </td> <td> <p>R<sub>35”</sub></p> </td> </tr> </tbody> </table> <p> </p> <table> <tbody> <tr> <td> <p>Data set on Zenodo</p> </td> <td> <p>X08_02</p> </td> <td> <p>X11_02</p> </td> <td> <p>X12_02</p> </td> <td> <p>X14_02</p> </td> <td> <p>X13_04</p> </td> <td> <p>X13_02</p> </td> <td> <p>X12_06</p> </td> <td> <p>X06_09</p> </td> <td> <p>X09_04</p> </td> <td> <p>X12_04</p> </td> <td> <p>X06_07</p> </td> <td> <p>X13_07</p> </td> </tr> <tr> <td> <p>Data set in Aumonier et al. 2022</p> </td> <td> <p>R<sub>51”</sub></p> </td> <td> <p>R<sub>62”</sub></p> </td> <td> <p>R<sub>62”</sub></p> </td> <td> <p>R<sub>67”</sub></p> </td> <td> <p>R<sub>72”</sub></p> </td> <td> <p>R<sub>80”</sub></p> </td> <td> <p>R<sub>90”</sub></p> </td> <td> <p>R<sub>130”</sub></p> </td> <td> <p>R<sub>166”</sub></p> </td> <td> <p>R<sub>258”</sub></p> </td> <td> <p>R<sub>630”</sub></p> </td> <td> <p>R<sub>1620”</sub></p> </td> </tr> </tbody> </table> <p>One dataset consists of a master file, four data files and two metadata files.</p>
Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM
<p>This respository corresponds to the following paper: Wankowicz et al. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM (2024). These are the qFit models. MTZ and deposited models cna be downloaded from the PDB. </p>
Cryo-EM and X-ray crystallography ligands represented as 3D voxel grids for training deep learning models
<p>Ligand datasets used to train and evaluate the models studied in <em>"Ligand Identification using Deep Learning</em><em>"</em> by Karolczak, J. <em>et al.</em></p> <p>The blobs_full.tar.gz and cryoem_blobs.zip files contain compressed 3D numpy arrays (*.npz) of all the ligand blobs extracted from X-ray and cryo-EM PDB deposits prior to quality filtering. The npz file names correspond to the PDB ID, chain, residue number, and ligand name of the extracted blob. The cmb_data.csv file contains the tabular data used to train the CheckMyBlob model. The X-ray data were later divided into training and testing subsets according to the xray_train.csv and xray_holdout.csv files, respectively. The ligand_mapping.csv file contains the mapping from ligand IDs to ligand group names. Finally, the cryoem_qscores.csv file contains Q-scores that were used to filter cryo-EM ligands.</p>
Expression test and purification of SETDB1 catalytic domain constructs' for structural studies by X-ray crystallography.
<p><strong>Experiment: </strong>Expression test and purification of SETDB1 catalytic domain constructs’ for structural studies by X-ray crystallography.</p> <p><strong>Aim:</strong> In the present section of this study, we focused on the development of efficient bacterial expression systems to produce large amounts of soluble SETDB1 catalytic domain for structural studies. This report involves a summary of expression test results of different fragments of SETDB1 and purification of various fusion proteins.</p>
X-ray crystallography datasets for the F420-reducing sulfite-reductase from Methanocaldococcus jannaschii and Methanothermococcus thermolithotrophicus
<p>The three datasets present in this entry are all related to X-ray crystallography data collected from crystals of the F<sub>420</sub>-reducing sulfite-reductase (Fsr) from <em>Methanocaldococcus jannaschii</em> (Mj) and <em>Methanothermococcus thermolithotrophicus</em> (Mt).</p> <p>MjFsr_Fe_Kedge.zip: Dataset collected at a wavelength of 1.74013 Å. Fsr from <em>Methanocaldococcus jannaschii.</em></p> <p>MjFsr.zip: Dataset collected at a wavelength of 0.97857 Å. Fsr from <em>Methanocaldococcus jannaschii.</em></p> <p>MtFsr.zip: Datasets collected at a wavelength of 1.00004 Å. Fsr from <em>Methanothermococcus thermolithotrophicus.</em></p>
Body temperature protein X-ray crystallography at 37°C: A rhenium protein complex seeking a physiological condition structure: Raw Diffraction Images (112 week soak) Zenodo
<p>The labratory dataset of the raw diffraction images obtained after 112 weeks of soaking in the mother liquor and collected at a wavelength of 1.54 Å, illustrating the covalent coordination of the rhenium(I) tricarbonyl fragment to the His and Asp amino acid residues as well as other similarities when comparing the 37°C data set to 100K data set as described in the publication titled "Body temperature protein X-ray crystallography at 37°C: A rhenium protein complex seeking a physiological condition structure", written by Jacobs, Helliwell & Brink,<em> ChemComm</em>, 2024.</p> <p>The raw diffraction images for the labratory data sets are made available at the Zenodo research data archive, as specified in the publication.</p>
Mixed chirality α-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography
<p>The upload contains additional primary data associated with the publication <a href="https://doi.org/10.1039/D1CB00124H">https://doi.org/10.1039/D1CB00124H</a>, including raw data in the original file format whenever possible.</p> <p>Data content: HPLC-MS, CD, Vesicle leakage, Molecular Dynamics, Crystallography (primary electron density maps) and Supporting Information.</p>
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International Brain Laboratory public data
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OpenNeuro
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