X-Ray Diffraction data from Human receptor NKR-P1 in glycosylated form, extracellular domain, source of 5MGR structure

Data DOI: 10.15785/SBGRID/778 | ID: 778

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

Dohnalek Laboratory, Institute of Biotechnology of the Czech Academy of Sciences

Release Date: May 13, 2022

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/778

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/778 .' (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/778 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/778 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/778 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 778 ; shasum -c files.sha'

Storage requirements: 42G

Biological Sample:

Human receptor NKR-P1 in glycosylated form, extracellular domain

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

Diamond beam line I03

Data Creation Date:

May 7, 2015

Related Datasets:

None


Cite this Dataset

Skalova, T; Blaha, J; Harlos, K; Hasek, J; Koval, T; Stransky, J; Vanek, O; Yuguang, Z; Dohnalek, J. 2022. "X-Ray Diffraction data for: Human receptor NKR-P1 in glycosylated form, extracellular domain. PDB Code 5MGR", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/778.

Download Citation

Dataset Description

native data set

Project Members

Name Additional Roles Affiliation While Working on the Project
Tereza SkalovaData Collector, DepositorInstitute of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50, Vestec, Czech Republic
Jan BlahaData CollectorDepartment of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic
Jan DohnalekData CollectorInstitute of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50, Vestec, Czech Republic
Karl HarlosData CollectorDivision of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
Jindrich HasekData CollectorInstitute of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50, Vestec, Czech Republic
Tomas KovalData CollectorInstitute of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50, Vestec, Czech Republic
Jan StranskyData CollectorInstitute of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50, Vestec, Czech Republic
Ondrej VanekData CollectorDepartment of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic
Zhao YuguangData CollectorDivision of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
Jan DohnalekPIInstitute of Biotechnology of the Czech Academy of Sciences

Reprocessing Instructions

used all images 1-7200

Reprocessing Data

About Reprocessing

Version:

version unreported

Reprocessing failed.

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97625

Sweep:

SWEEP1

Files:

/programs/datagrid/778/565101-C12-x1_2_####.cbf

Images:

1 - 7200

Beam:

(208.26, 215.7) -> (208.26, 215.73)

Distance:

340.05 -> 340.55

Spacegroup:

P 31 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.58 4.29 1.58
Low resolution limit 53.81 53.84 1.61
Completeness 99.9 100.0 97.0
Multiplicity 35.0 35.5 16.5
I/sigma 30.6 96.0 0.6
Rmerge 0.057 0.037 3.241
CC half 1.0 1.0 0.284
Anomalous completeness 99.7 100.0 95.9
Anomalous multiplicity 18.4 18.4 18.4
Cell 68.51 68.51 127.76 90.0 90.0 120.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97625

Sweep:

SWEEP1

Files:

/programs/datagrid/778/565101-C12-x1_2_####.cbf

Images:

1 - 7200

Beam:

(208.26, 215.7) -> (208.26, 215.73)

Distance:

340.05 -> 342.12

Spacegroup:

P 31 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.58 4.29 1.58
Low resolution limit 127.85 128.27 1.61
Completeness 99.9 100.0 97.0
Multiplicity 35.0 35.5 16.5
I/sigma 30.6 96.0 0.6
Rmerge 0.057 0.037 3.255
CC half 1.0 1.0 0.263
Anomalous completeness 99.7 100.0 95.9
Anomalous multiplicity 18.4 18.4 18.4
Cell 68.51 68.51 127.85 90.0 90.0 120.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97625

Sweep:

SWEEP1

Files:

/programs/datagrid/778/565101-C12-x1_2_####.cbf

Images:

1 - 7200

Beam:

(208.26, 215.7) -> (208.26, 215.73)

Distance:

340.05 -> 341.53

Spacegroup:

P 31 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.52 4.13 1.52
Low resolution limit 127.65 128.1 1.55
Completeness 98.8 100.0 87.4
Multiplicity 31.4 35.9 11.7
I/sigma 24.9 124.5 0.3
Rmerge 0.06 0.039 2.331
CC half 1.0 1.0 0.334
Anomalous completeness 98.2 100.0 83.4
Anomalous multiplicity 16.5 16.5 16.5
Cell 68.421 68.421 127.675 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.