SGC Oxford has performed a crystallographic fragment screen on the human peroxisomal coenzyme A diphosphatase NUDT7 (UniProtKB - P0C024). All structures with clearly identifiable ligands were deposited in the Protein Data Bank under Group Deposition ID G_1002045. The final structures and the relevant PanDDA event maps can be found at the SGC fragment screening website. This work is part of the Target Enabling Package (TEP) program at SGC and the complete TEP for NUDT7 is will also be available on ZENODO shortly.

Experiment

Crystals were prepared at the XChem facility of the Diamond Light Source (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the OxXChem set with nominal fragment concentrations of 100 mM, with DMSO at 30% v/v. Additionally, a series of follow-up compounds based on an initial fragment hit was synthesized and soaked overnight with nominal compound concentrations of 30 mM, with DMSO at 30% v/v. All datasets were collected at MX beamlines at DLS. Autoprocessed datasets were analysed by Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). All ligands that were clearly identifiable in PanDDA event maps were modelled, refined and deposited into the PDB.

Content

This repository contains:

all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event & Z-maps for all ligand bound structures

MTZ and AIMLESS logfiles from auto-processing

PDB, CIF & PNG files of all the soaked compounds

final refine.pdb and refine.mtz filess of all ligand bound structures

all data belonging to an individual crystal can be found in processed_datasets/

References

Cox, O. B. et al. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci. 7, 2322–2330 (2016).

Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).

Interactive summary page for "PanDDA analysis of BAZ2B screened against Zenobia Fragment Library".

Please click on "0_index.html" in the "Files" section to open the interactive summary.

All datasets are also available as combined zip files from https://zenodo.org/record/48768 .

Interactive summary page for "PanDDA analysis of JMJD2D screened against Zenobia Fragment Library".

Please click on "0_index.html" in the "Files" section to open the interactive summary.

All datasets are also available as combined zip files from https://zenodo.org/record/48770 .

Nulear auto-antigen SP-100 screened against a selection of the Maybridge Fragment Library by X-ray crystallography.

The main entity of this document is a structure with accession number 5qo9

This deposition contains the X-ray diffraction data used for the PanDDA analysis of the fragment screen against the NSP3 macrodomain of SARS-CoV-2 described in Schuller et al. 2021 (DOI: 10.1126/sciadv.abf8711).

A description of the files can be found in the "README" text file.

The data in this deposition is from the fragment screen performed at UCSF using P43 crystals. The data from the fragment screen performed at UCSF using C2 crystals can be found here - https://zenodo.org/record/4716363 - in the zipped directory named "ucsf_nsp3_mac1_C2.zip".

Interactive summary page for "PanDDA analysis of SP100 screened against selection of Maybridge Fragment Library".

Please click on "0_index.html" in the "Files" section to open the interactive summary.

All datasets are also available as combined zip files from https://zenodo.org/record/48771 .

Bromodomain BAZ2B screened against the Zenobia Fragment Library by X-ray Crystallography.

Reanalysis of PTP1B screened against multiple fragment libraries via X-ray crystallography using the XChem pipeline. The data was pre-clustered via cluster4x and then analyzed via PanDDA.

The main entity of this document is a structure with accession number 5qgx

Red Panda

## Overview

Red Panda is a dataset for object detection tasks - it contains Red Panda annotations for 756 images.

## Getting Started

You can download this dataset for use within your own projects, or fork it into a workspace on Roboflow to create your own model.

  ## License

  This dataset is available under the [CC BY 4.0 license](https://creativecommons.org/licenses/CC BY 4.0).

The main entity of this document is a structure with accession number 5qjm

PTP1B re-screened against multiple fragment libraries with RT crystallography

A crystallographic fragment screen against the nsp10-nsp14 ExoN heterodimeric complex was performed at the FragMAX facility (MAX IV Laboratory). Crystals were soaked with compounds from the FragMAXlib library and about half of the crystals screened belonged to space group P21. This repository contains a tar archive file of all files generated during the corresponding Pan-Dataset Density Analysis (PanDDA, 10.1038/ncomms15123) analysis of the respective datasets. The following PDB accession codes are associated with datasets collected during this campaign:
• 9FWI (NSP1014-x0055)
• 9FWK (NSP1014-x0083)
• 9FWL (NSP1014-x0098)
• 9FWM (NSP1014-x0103)
• 9FWS (NSP1014-x0158)
• 9FWT (NSP1014-x0159)
• 9FWU (NSP1014-x0186)
Two datasets that had only weakly bound fragment, i.e. fragments that could only be identified in PanDDA event maps, bit not in not be identified in 2fofc electron density and fofc difference electron density maps. These datasets were additionally analysed with the Xtrapol8 algorithm (10.1038/s42003-022-03575-7) and the full analysis was also uploaded to zenodo:
• NSP1014-x0055: 10.5281/zenodo.11182330
• NSP1014-x0083: 10.5281/zenodo.11182339
• NSP1014-x0159: 10.5281/zenodo.11182341

Bromodomain BRD1 screened against the 3D Fragment Consortium Fragment Library by X-ray Crystallography.

PANDA is the first gigaPixel-level humAN-centric viDeo dAtaset, for large-scale, long-term, and multi-object visual analysis. The videos in PANDA were captured by a gigapixel camera and cover real-world scenes with both wide field-of-view (~1 square kilometer area) and high-resolution details (~gigapixel-level/frame). The scenes may contain 4k head counts with over 100x scale variation. PANDA provides enriched and hierarchical ground-truth annotations, including 15,974.6k bounding boxes, 111.8k fine-grained attribute labels, 12.7k trajectories, 2.2k groups and 2.9k interactions.

The main entity of this document is a structure with accession number 5r8p

Fiat Automobiles S.p.A is an Italian automobile manufacturer and part of Fiat Chrysler Automobiles which was founded in 1899. The Fiat Panda has been in production since 1980. Between 2008 and 2020, the total sales of Fiat Panda cars in the Netherlands peaked in 2010 at roughly 10,500 cars. Over the following years Fiat Panda sales decreased annually, and in 2020 just over 385 Fiat Pandas were sold in the Netherlands.

Founder and habitat contributions to the captive panda population. (XLSX 100 kb)

Dataset

This dataset was created by Do Huynh

Contents