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

dataset logo thumbnail
Visualize in 3D >>

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.

Download Citation

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 3.0 8.15 3.0
Low resolution limit 64.33 64.34 3.05
Completeness 98.3 100.0 82.9
Multiplicity 3.7 6.0 3.4
I/sigma 3.2 24.1 0.9
Rmerge 0.871 0.311 0.876
CC half 0.148 0.831 0.06
Anomalous completeness 94.3 98.7 79.7
Anomalous multiplicity 1.9 1.9 1.9
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.