X-Ray Diffraction data from Hen Lysozyme, source of 8DYZ structure

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: Sept. 9, 2022

Data Access Instructions

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:


Collection Facility:

CHESS Beamline F1

Data Creation Date:

June 25, 2017

Related Datasets:


Cite this Dataset

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.

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Dataset Description

Hen lysozyme in tetragonal space group at ambient temperature, diffuse scattering dataset

Project Members

Name Additional Roles Affiliation While Working on the Project
Steve P MeisburgerData Collector, DepositorCornell University and Princeton University
Nozomi AndoData CollectorCornell University and Princeton University
Nozomi AndoPICornell University

Reprocessing Instructions

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

License and Terms of use

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.