X-Ray Diffraction data from complex of engineered human chemokine CX3CL1 with viral US28 and two nanobodies, source of 5WB2 structure

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Data DOI: 10.15785/SBGRID/582 | ID: 582

Publication DOI: 10.7554/eLife.35850

5WB2 Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Garcia Laboratory, Stanford University

Release Date: 8 Jun 2018

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/582

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/582 .' (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/582 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/582 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/582 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 582 ; shasum -c files.sha'

Storage requirements: 21G

Biological Sample:

complex of engineered human chemokine CX3CL1 with viral US28 and two nanobodies

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

APS 23 ID-D

Data Creation Date:

7 Aug 2016

Related Datasets:

None


Cite this Dataset

Jude, KM; Garcia, KC; Tsutsumi, N; Garcia, K. 2018. "X-Ray Diffraction data for: complex of engineered human chemokine CX3CL1 with viral US28 and two nanobodies. PDB Code 5WB2", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/582.

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Dataset Description

datasets merged from 2 crystals

Project Members

Name Additional Roles Affiliation While Working on the Project
Kevin M JudeData Collector, DepositorStanford University/Howard Hughes Medical Institute
K C GarciaStanford University/Howard Hughes Medical Institute
Naotaka TsutsumiData CollectorStanford University
K. Christopher GarciaPIStanford University

Reprocessing Instructions

used xds to process first 200 frames of 0344B3_5_?????.cbf and frames 450-1050 of 0343D3_1_?????.cbf and merged with xscale

Reprocessing Data

About Reprocessing

xia2 -2d

xia2 -3d

xia2 -3dii

xia2 -dials
/programs/x86_64-linux/dials/1.8.5/dials-1.8.5/build/bin/xia2 pipeline=2d /programs/datagrid//582/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/1.8.5/dials-1.8.5/build/bin/xia2 pipeline=3d /programs/datagrid//582/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/1.8.5/dials-1.8.5/build/bin/xia2 pipeline=3dii /programs/datagrid//582/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/1.8.5/dials-1.8.5/build/bin/xia2 pipeline=dials /programs/datagrid//582/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.03323

Sweep:

SWEEP2

Files:

/programs/datagrid/582/0344B3_5_#####.cbf

Images:

1 - 1800

Beam:

(221.54, 214.48) -> (221.54, 214.92)

Distance:

450.0 -> 451.3

Spacegroup:

P 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 3.03 8.23 3.03
Low resolution limit 64.33 64.34 3.09
Completeness 98.3 97.5 84.4
Multiplicity 3.1 4.9 2.6
I/sigma 3.0 27.6 0.6
Rmerge 1.0 0.325 1.0
CC half 0.0 0.119 -0.003
Anomalous completeness 91.8 94.2 75.3
Anomalous multiplicity 1.6 1.6 1.6
Cell 47.423 127.248 128.656 89.838 90.05 89.741

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.