X-Ray Diffraction data from Nicotiana suaveolens defensin 7 in complex with PIP2, source of 5VYP structure

Data DOI: 10.15785/SBGRID/461 | ID: 461

Publication DOI: 10.1002/1873-3468.12761

5VYP Coordinates: Viewer, PDB, MMDB

Kvansakul Laboratory, La Trobe University

Release Date: 4 Aug 2017

Data Access Instructions

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


Cite this Dataset

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, http://dx.doi.org/10.15785/SBGRID/461.

Download Citation

Dataset Description

Native dataset

Project Members

Name Additional Roles Affiliation While Working on the Project
Michael JarvaData Collector, DepositorDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
Mark D HulettDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
Marc KvansakulData CollectorDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
Fung T LayDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
Marc KvansakulPILa Trobe University

Reprocessing Instructions

Frames 1-135 processed in XDS and then merged in Aimless.

Reprocessing Data

About Reprocessing

Version:

version unreported

Reprocessing failed.

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 -> 350.09

Spacegroup:

P 1 21 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.76 7.47 2.76
Low resolution limit 38.74 38.75 2.81
Completeness 100.0 99.9 100.0
Multiplicity 7.6 7.3 7.6
I/sigma 8.5 26.8 1.3
Rmerge 0.212 0.051 1.564
CC half 0.991 0.998 0.457
Anomalous completeness 99.9 99.9 99.7
Anomalous multiplicity 3.9 3.9 3.9
Cell 75.42 83.4 105.03 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 -> 350.23

Spacegroup:

P 1 21 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.76 7.48 2.76
Low resolution limit 44.51 44.52 2.81
Completeness 100.0 99.8 100.0
Multiplicity 7.6 7.3 7.6
I/sigma 8.5 26.8 1.3
Rmerge 0.213 0.051 1.588
CC half 0.991 0.998 0.432
Anomalous completeness 99.9 99.7 99.8
Anomalous multiplicity 3.9 3.9 3.9
Cell 75.49 83.48 105.12 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 -> 348.63

Spacegroup:

P 1 21 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.67 7.23 2.67
Low resolution limit 83.1 83.14 2.71
Completeness 99.6 100.0 91.0
Multiplicity 7.5 7.4 7.6
I/sigma 6.5 16.6 1.0
Rmerge 0.238 0.066 1.91
CC half 0.992 0.999 0.461
Anomalous completeness 99.6 100.0 91.1
Anomalous multiplicity 3.8 3.8 3.8
Cell 75.164 83.101 104.673 90.0 94.029 90.0

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.