Data DOI: 10.15785/SBGRID/461 | ID: 461
Publication DOI: 10.1002/1873-3468.12761
5VYP Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB
Kvansakul Laboratory, La Trobe University
Release Date: 4 Aug 2017
1. If this dataset is locally available, it should be accessable at /programs/datagrid/461
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/461 .' (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/461 .' (Uppsala University, Sweden)
'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/461 .' (Institut Pasteur de Montevideo, Uruguay)
'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/461 .' (Shanghai Institutes for Biological Sciences, China)
3. After the transfer is completed, please issue the following command to verify data integrity:
'cd 461 ; shasum -c files.sha'
Storage requirements: 6.4G
Biological Sample:
Nicotiana suaveolens defensin 7 in complex with PIP2
Dataset Type:
X-Ray Diffraction
Subject Composition:
Ligand, Protein
Collection Facility:
MX-2, Australian Synchrotron, Melbourne, Australia
Data Creation Date:
7 Dec 2016
Related Datasets:
None
Jarva, M; Hulett, MD; Lay, FT; Kvansakul, M. 2017. "X-Ray Diffraction data for: Nicotiana suaveolens defensin 7 in complex with PIP2. PDB Code 5VYP", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/461.
Native dataset
| Name | Additional Roles | Affiliation While Working on the Project |
|---|---|---|
| Michael Jarva | Data Collector, Depositor | Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. |
| Mark D Hulett | Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. | |
| Marc Kvansakul | Data Collector | Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. |
| Fung T Lay | Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. | |
| Marc Kvansakul | PI | La Trobe University |
Frames 1-135 processed in XDS and then merged in Aimless.
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.9537
Sweep:
SWEEP1
Files:
/programs/datagrid/461/1137_NsD7PIP2b_1_###.img
Images:
1 - 360
Beam:
(158.71, 156.93) -> (158.71, 157.12)
Distance:
350.02 -> 350.24
Spacegroup:
P 1 21 1
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 2.62 | 7.1 | 2.62 |
| Low resolution limit | 38.71 | 38.71 | 2.67 |
| Completeness | 100.0 | 98.9 | 100.0 |
| Multiplicity | 7.5 | 7.0 | 7.6 |
| I/sigma | 7.3 | 24.1 | 0.9 |
| Rmerge | 0.25 | 0.053 | 2.241 |
| CC half | 0.99 | 0.999 | 0.307 |
| Anomalous completeness | 99.7 | 98.8 | 99.7 |
| Anomalous multiplicity | 3.8 | 3.8 | 3.8 |
| Cell | 75.35 | 83.32 | 104.93 | 90.0 | 94.01 | 90.0 |
|---|
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.9537
Sweep:
SWEEP1
Files:
/programs/datagrid/461/1137_NsD7PIP2b_1_###.img
Images:
1 - 360
Beam:
(158.71, 156.93) -> (158.71, 157.13)
Distance:
350.02 -> 349.53
Spacegroup:
P 1 21 1
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 2.62 | 7.11 | 2.62 |
| Low resolution limit | 50.35 | 50.35 | 2.67 |
| Completeness | 99.9 | 98.6 | 100.0 |
| Multiplicity | 7.5 | 7.0 | 7.6 |
| I/sigma | 7.3 | 24.1 | 0.9 |
| Rmerge | 0.25 | 0.053 | 2.238 |
| CC half | 0.99 | 0.999 | 0.306 |
| Anomalous completeness | 99.7 | 98.5 | 99.7 |
| Anomalous multiplicity | 3.8 | 3.8 | 3.8 |
| Cell | 75.35 | 83.32 | 104.93 | 90.0 | 94.01 | 90.0 |
|---|
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.9537
Sweep:
SWEEP1
Files:
/programs/datagrid/461/1137_NsD7PIP2b_1_###.img
Images:
1 - 360
Beam:
(158.71, 156.93) -> (158.71, 157.12)
Distance:
350.02 -> 348.84
Spacegroup:
P 1 2 1
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 1.97 | 5.35 | 1.97 |
| Low resolution limit | 83.15 | 83.23 | 2.0 |
| Completeness | 93.2 | 100.0 | 58.9 |
| Multiplicity | 6.7 | 5.8 | 4.3 |
| I/sigma | 28.6 | 35.3 | 15.6 |
| Rmerge | 0.094 | 0.061 | 0.136 |
| CC half | 0.85 | 0.863 | 0.091 |
| Anomalous completeness | 92.9 | 100.0 | 57.8 |
| Anomalous multiplicity | 3.4 | 3.4 | 3.4 |
| Cell | 75.216 | 83.152 | 104.77 | 90.0 | 94.021 | 90.0 |
|---|
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.
