X-Ray Diffraction data from Hen Lysozyme, source of 8DZ7 structure

Data DOI: 10.15785/SBGRID/958 | ID: 958

Publication DOI: 10.1101/2022.08.22.504832

8DZ7 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/958

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/958 .' (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/958 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/958 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/958 .' (Shanghai Institutes for Biological Sciences, China)

3. After the transfer is completed, please issue the following command to verify data integrity:

'cd 958 ; 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:

March 17, 2016

Related Datasets:


Cite this Dataset

Meisburger, SP; Imran, SM.S.; Ando, N. 2022. "X-Ray Diffraction data for: Hen Lysozyme. PDB Code 8DZ7", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/958.

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Dataset Description

Hen lysozyme in orthorhombic 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
Syed M.S. ImranData CollectorPrinceton University
Nozomi AndoPICornell University

Reprocessing Instructions

The deposition consists of 4000 diffraction images from two large crystals (prefixes lys_rt_2 and lys_rt_5) collected at ambient temperature. For each crystal, there are four sweeps of 50 degrees each collected from separate locations to spread the dose. File name templates are as follows: First crystal: lys_rt_2_NN_????.cbf where NN=38-41 Second crystal: lys_rt_5_NN_????.cbf where NN=51-54 In addition, there are background datasets for each crystal, where the crystal has been translated out of the beam along the spindle axis. Background templates are lys_rt_2_42_????.cbf and lys_rt_5_55_????.cbf (first and second crystal respectively). The backgrounds can be matched up with crystal images using the phi value in the image header. The data processing procedure that resulted in the refined structure involved integration using XDS for each sweep, then merging sweeps using Aimless. A reciprocal space reconstruction was generated from the raw data (including background images) using custom MATLAB code (https://github.com/ando-lab/mdx-lib) as described in the publication. The diffraction data can be re-processed using xia2 as follows: xia2 pipeline=dials xia2.settings.space_group=P212121 image=lys_rt_2_38_0001.cbf image=lys_rt_2_39_0001.cbf image=lys_rt_2_40_0001.cbf image=lys_rt_2_41_0001.cbf image=lys_rt_5_51_0001.cbf image=lys_rt_5_52_0001.cbf image=lys_rt_5_53_0001.cbf image=lys_rt_5_54_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.