Data DOI: 10.15785/SBGRID/957 | ID: 957
Publication DOI: 10.1101/2022.08.22.504832
8DYZ Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB
Ando Laboratory, Cornell University
Release Date: 9 Sep 2022
1. If this dataset is locally available, it should be accessable at /programs/datagrid/957
2. To download this dataset, please run the following command from your Terminal on a Linux or OS X workstation:
'rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/957 .'
(Harvard Medical School, USA)
Depending on your location, faster access may be available from a Tier 1 site closer to your location
'rsync -av rsync://sbgrid.icm.uu.se/10.15785/SBGRID/957 .'
(Uppsala University, Sweden)
'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/957 .'
(Institut Pasteur de Montevideo, Uruguay)
'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/957 .'
(Shanghai Institutes for Biological Sciences, China)
3. After the transfer is completed, please issue the following command to verify data integrity:
'cd 957 ; shasum -c files.sha'
Storage requirements: 26G
Biological Sample:
Hen Lysozyme
Dataset Type:
X-Ray Diffraction
Subject Composition:
Protein
Collection Facility:
CHESS Beamline F1
Data Creation Date:
25 Jun 2017
Related Datasets:
None
Meisburger, SP; Ando, N. 2022. "X-Ray Diffraction data for: Hen Lysozyme. PDB Code 8DYZ", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/957.
Hen lysozyme in tetragonal space group at ambient temperature, diffuse scattering dataset
Name | Additional Roles | Affiliation While Working on the Project |
---|---|---|
Steve P Meisburger | Data Collector, Depositor | Cornell University and Princeton University |
Nozomi Ando | Data Collector | Cornell University and Princeton University |
Nozomi Ando | PI | Cornell University |
This deposition includes 4000 X-ray images collected from one large crystal at ambient temperature. The images are divided into eight wedges of 50 degrees each (the crystal was translated between wedges to distribute the dose) with file name templates lys_1_N_????.cbf where N is 2-9. Additionally, 360 background images are included (template lys_1_bkg_1_????.cbf) corresponding to a full 360 degree rotation with the crystal translated out of the beam. The background images can be matched with corresponding frames using the phi value in the image headers. The data processing routine that resulted in the deposited structure involved integrating each wedge using XDS followed by merging in Aimless. Reciprocal space maps were generated using custom MATLAB code (https://github.com/ando-lab/mdx-lib) using both the diffraction and background images, the procedures for which are described in the publication. The data can also be re-processed using xia2 as follows: xia2 pipeline=dials xia2.settings.space_group=P43212 image=lys_1_2_0001.cbf image=lys_1_3_0001.cbf image=lys_1_4_0001.cbf image=lys_1_5_0001.cbf image=lys_1_6_0001.cbf image=lys_1_7_0001.cbf image=lys_1_8_0001.cbf image=lys_1_9_0001.cbf
Version:
version unreported
Reprocessing failed.
Version:
version unreported
Reprocessing failed.
Version:
version unreported
Reprocessing failed.
License: CC0
Terms: Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation, as generated by the SBGrid Data Bank.