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: 20 Jan 2017
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:
19 Apr 2016
Related Datasets:
None
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.
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.
| Name | Additional Roles | Affiliation While Working on the Project |
|---|---|---|
| Shouqiang Cheng | Data Collector | University of Chicago |
| Engin Ozkan | Data Collector, Depositor, PI | University of Chicago |
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.
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 -> 696.06
Spacegroup:
P 62 2 2
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 3.93 | 10.66 | 3.93 |
| Low resolution limit | 89.71 | 89.73 | 4.0 |
| Completeness | 100.0 | 100.0 | 100.0 |
| Multiplicity | 8.6 | 7.3 | 8.8 |
| I/sigma | 9.1 | 40.9 | 1.1 |
| Rmerge | 0.183 | 0.033 | 1.988 |
| CC half | 0.998 | 0.999 | 0.29 |
| Anomalous completeness | 99.9 | 99.7 | 99.9 |
| Anomalous multiplicity | 4.7 | 4.7 | 4.7 |
| Cell | 179.42 | 179.42 | 214.53 | 90.0 | 90.0 | 120.0 |
|---|
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 -> 697.87
Spacegroup:
P 62 2 2
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 3.94 | 10.69 | 3.94 |
| Low resolution limit | 89.71 | 89.73 | 4.01 |
| Completeness | 100.0 | 100.0 | 100.0 |
| Multiplicity | 8.6 | 7.4 | 8.9 |
| I/sigma | 9.2 | 40.8 | 1.2 |
| Rmerge | 0.182 | 0.033 | 1.879 |
| CC half | 0.998 | 0.999 | 0.334 |
| Anomalous completeness | 99.9 | 99.7 | 99.9 |
| Anomalous multiplicity | 4.7 | 4.7 | 4.7 |
| Cell | 179.42 | 179.42 | 214.53 | 90.0 | 90.0 | 120.0 |
|---|
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 -> 697.46
Spacegroup:
P 62 2 2
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 3.78 | 10.25 | 3.78 |
| Low resolution limit | 73.04 | 73.05 | 3.85 |
| Completeness | 100.0 | 100.0 | 99.9 |
| Multiplicity | 8.6 | 7.6 | 8.9 |
| I/sigma | 8.2 | 47.6 | 0.7 |
| Rmerge | 0.182 | 0.039 | 2.117 |
| CC half | 0.998 | 0.999 | 0.201 |
| Anomalous completeness | 100.0 | 100.0 | 99.8 |
| Anomalous multiplicity | 4.7 | 4.7 | 4.7 |
| Cell | 179.4 | 179.4 | 214.433 | 90.0 | 90.0 | 120.0 |
|---|
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.
