Data DOI: 10.15785/SBGRID/753 | ID: 753
Publication DOI: 10.3390/cancers12071998
6YJP Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB
Dohnalek Laboratory, Institute of Biotechnology of the Czech Academy of Sciences
Release Date: 17 Jul 2020
1. If this dataset is locally available, it should be accessable at /programs/datagrid/753
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/753 .' (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/753 .' (Uppsala University, Sweden)
'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/753 .' (Institut Pasteur de Montevideo, Uruguay)
'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/753 .' (Shanghai Institutes for Biological Sciences, China)
3. After the transfer is completed, please issue the following command to verify data integrity:
'cd 753 ; shasum -c files.sha'
Storage requirements: 95G
Biological Sample:
NKp30 in complex with B7H6
Dataset Type:
X-Ray Diffraction
Subject Composition:
Protein
Collection Facility:
Diamond, beamline I02
Data Creation Date:
29 Jun 2016
Related Datasets:
None
Skalova, T; Harlos, K; Skorepa, O; Vanek, O; Dohnalek, J. 2020. "X-Ray Diffraction data for: NKp30 in complex with B7H6. PDB Code 6YJP", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/753.
six data sets (six crystals) used for merging and molecular replacement (no experimental phasing)
| Name | Additional Roles | Affiliation While Working on the Project |
|---|---|---|
| Tereza Skalova | Data Collector, Depositor | Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50, Vestec, Czech Republic |
| Jan Dohnalek | Data Collector | Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50, Vestec, Czech Republic |
| Karl Harlos | Data Collector | Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN Oxford, United Kingdom |
| Ondrej Skorepa | Data Collector | Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic |
| Ondrej Vanek | Data Collector | Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic |
| Jan Dohnalek | PI | Institute of Biotechnology of the Czech Academy of Sciences |
Merging strategies tested: 1) B7x1 (800 images), B8x5 (800 images) and B8x3 (450 images), 3.1A in C2; 2) B6x2 (800), B7x1 (1800), B8x2 (2400), B8x3 (2200), B8x4 (2100), B8x5 (1800), 3.4A in P1; Finally, three data sets (B7x1: images 1 to 800, B8x5:1 to 800, and B8x3:1 to 450) were merged with the best results (space group C2, 3.1A).
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.97949
Sweep:
SWEEP6
Files:
/programs/datagrid/753/605982-B8-x4/605982-B8-x4_2_####.cbf
Images:
1 - 3600
Beam:
(220.0, 212.48) -> (220.0, 212.56)
Distance:
669.64 -> 671.23
Spacegroup:
P 1
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 2.27 | 6.17 | 2.27 |
| Low resolution limit | 68.17 | 68.2 | 2.31 |
| Completeness | 47.6 | 96.4 | 10.5 |
| Multiplicity | 7.7 | 10.8 | 1.8 |
| I/sigma | 4.6 | 20.4 | -0.1 |
| Rmerge | 1.098 | 0.584 | -5.068 |
| CC half | 0.584 | 0.473 | -0.057 |
| Anomalous completeness | 40.4 | 88.3 | 7.4 |
| Anomalous multiplicity | 4.2 | 4.2 | 4.2 |
| Cell | 86.26 | 100.44 | 111.11 | 83.54 | 90.0 | 72.46 |
|---|
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.97949
Sweep:
SWEEP6
Files:
/programs/datagrid/753/605982-B8-x4/605982-B8-x4_2_####.cbf
Images:
1 - 3600
Beam:
(220.0, 212.48) -> (220.0, 212.57)
Distance:
669.64 -> 672.35
Spacegroup:
C 1 2 1
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 3.1 | 8.41 | 3.1 |
| Low resolution limit | 82.2 | 82.23 | 3.15 |
| Completeness | 100.0 | 100.0 | 99.5 |
| Multiplicity | 26.3 | 27.5 | 3.6 |
| I/sigma | 10.2 | 44.5 | 0.3 |
| Rmerge | 0.212 | 0.07 | 2.608 |
| CC half | 0.999 | 0.999 | 0.311 |
| Anomalous completeness | 99.0 | 100.0 | 84.2 |
| Anomalous multiplicity | 13.6 | 13.6 | 13.6 |
| Cell | 165.87 | 86.4 | 111.3 | 90.0 | 97.64 | 90.0 |
|---|
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.97949
Sweep:
SWEEP6
Files:
/programs/datagrid/753/605982-B8-x4/605982-B8-x4_2_####.cbf
Images:
1 - 3600
Beam:
(220.0, 212.48) -> (220.0, 212.57)
Distance:
669.64 -> 669.44
Spacegroup:
C 1 2 1
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 3.02 | 8.2 | 3.02 |
| Low resolution limit | 110.3 | 110.37 | 3.07 |
| Completeness | 99.8 | 100.0 | 96.3 |
| Multiplicity | 29.1 | 29.1 | 20.5 |
| I/sigma | 6.3 | 41.4 | 0.1 |
| Rmerge | 0.258 | 0.107 | 7.986 |
| CC half | 0.998 | 0.997 | 0.604 |
| Anomalous completeness | 99.8 | 100.0 | 96.4 |
| Anomalous multiplicity | 14.9 | 14.9 | 14.9 |
| Cell | 166.127 | 86.448 | 111.285 | 90.0 | 97.644 | 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.
