X-Ray Diffraction data from Rat Glutamate receptor delta-2 extracellular domain, source of 5L2E structure

Data DOI: 10.15785/SBGRID/419 | ID: 419

Publication DOI: 10.1016/j.str.2016.11.004

5L2E Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Ozkan Laboratory, University of Chicago

Release Date: Jan. 20, 2017

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/419

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/419 .' (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/419 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/419 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/419 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 419 ; shasum -c files.sha'

Storage requirements: 2.4G

Biological Sample:

Rat Glutamate receptor delta-2 extracellular domain

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

Beamline 23-ID-D, GM/CA, APS, Chicago, IL

Data Creation Date:

April 19, 2016

Related Datasets:

None


Cite this Dataset

Cheng , S; Ozkan, E. 2017. "X-Ray Diffraction data for: Rat Glutamate receptor delta-2 extracellular domain. PDB Code 5L2E", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/419.

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Dataset Description

Anisotropic data, with diffraction varying from 3.5 A to 7 A. First 400 images of a 600-image dataset, remainder of which had to be removed due to radiation damage. Crystal is twinned with a twin fraction of 0.49 and twinning law -h, -k, l. True space group is P3(2)21, but appears as P6(x)22 due to twinning.

Project Members

Name Additional Roles Affiliation While Working on the Project
Shouqiang Cheng Data CollectorUniversity of Chicago
Engin OzkanData Collector, Depositor, PIUniversity of Chicago

Reprocessing Instructions

Processed well in HKL-2000 version 0.98.712 using automatic corrections at the scaling step. Beamline host-provided beam centers are: For XDS, ORGX=1244, ORGY=1297; for HKL-2000, x beam = 223.1 mm, y beam = 214.0 mm. Refined x/y beam values from HKL-2000 are 222.72, 215.1.

Reprocessing Data

About Reprocessing

Version:

version unreported

Reprocessing failed.

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.0332

Sweep:

SWEEP1

Files:

/programs/datagrid/419/A1_8_#####.cbf

Images:

1 - 400

Beam:

(223.26, 213.8) -> (223.26, 214.9)

Distance:

700.0 -> 702.73

Spacegroup:

P 62 2 2

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 5.56 15.07 5.56
Low resolution limit 88.28 88.29 5.66
Completeness 100.0 100.0 100.0
Multiplicity 8.2 6.5 8.9
I/sigma 19.4 41.6 5.6
Rmerge 0.075 0.03 0.396
CC half 0.999 0.999 0.915
Anomalous completeness 99.8 100.0 100.0
Anomalous multiplicity 4.7 4.7 4.7
Cell 179.43 179.43 214.54 90.0 90.0 120.0

Version:

version unreported

Reprocessing failed.

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.0332

Sweep:

SWEEP1

Files:

/programs/datagrid/419/A1_8_#####.cbf

Images:

1 - 400

Beam:

(223.26, 213.8) -> (223.26, 214.9)

Distance:

700.0 -> 697.59

Spacegroup:

P 62 2 2

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 3.81 10.34 3.81
Low resolution limit 88.23 88.25 3.88
Completeness 100.0 100.0 100.0
Multiplicity 8.3 7.3 8.5
I/sigma 8.3 32.2 1.2
Rmerge 0.187 0.04 2.014
CC half 0.998 0.999 0.251
Anomalous completeness 100.0 100.0 100.0
Anomalous multiplicity 4.5 4.5 4.5
Cell 179.363 179.363 214.401 90.0 90.0 120.0

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.