X-Ray Diffraction data from Virulence-associated protein VapB from the intracellular pathogen Rhodococcus equi, source of 7B1Z structure

Data DOI: 10.15785/SBGRID/987 | ID: 987

Publication DOI: 10.1107/S2053230X2100738X

7B1Z Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Niemann Laboratory, Bielefeld University

Release Date: Feb. 7, 2023

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/987

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/987 .' (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/987 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/987 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/987 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 987 ; shasum -c files.sha'

Storage requirements: 13G

Biological Sample:

Virulence-associated protein VapB from the intracellular pathogen Rhodococcus equi

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

beamline P14, operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany)

Data Creation Date:

Oct. 6, 2012

Related Datasets:

None


Cite this Dataset

Niemann, HH. 2023. "X-Ray Diffraction data for: Virulence-associated protein VapB from the intracellular pathogen Rhodococcus equi. PDB Code 7B1Z", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/987.

Download Citation

Dataset Description

native data

Project Members

Name Additional Roles Affiliation While Working on the Project
Hartmut H NiemannData Collector, DepositorBielefeld University, Department of Chemistry
Hartmut NiemannPIBielefeld University

Reprocessing Instructions

The folder contains two runs collected from the same crystal under mostly the same settings except for the distance. The first run has image root starting "nh30_4_01_" and a detector distance of 290 mm and consists of 321 images. The second run has image root starting "nh30_4b_01_" and a detector distance of 243 mm and consists of 1810 images. Both runs were scaled together with XSCALE using zero dose extrapolation giving the correct starting dose for the second run. The folder "processing_templates.zip" contains XDS.INP files for both runs and the XSCALE.INP file.

Processing Bundle

Reprocessing Data

About Reprocessing

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.23953

Sweep:

SWEEP2

Files:

/programs/datagrid/987/nh30_4b_01_#####.cbf

Images:

1 - 1810

Beam:

(216.89, 211.9) -> (216.89, 212.2)

Distance:

243.4 -> 244.72

Spacegroup:

C 2 2 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.53 4.15 1.53
Low resolution limit 28.92 28.93 1.56
Completeness 94.1 100.0 57.9
Multiplicity 6.3 7.0 2.4
I/sigma 17.5 59.2 0.5
Rmerge 0.041 0.024 2.037
CC half 1.0 1.0 0.342
Anomalous completeness 90.4 99.7 42.8
Anomalous multiplicity 3.3 3.3 3.3
Cell 56.96 65.35 124.33 90.0 90.0 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.23953

Sweep:

SWEEP2

Files:

/programs/datagrid/987/nh30_4b_01_#####.cbf

Images:

1 - 1810

Beam:

(216.89, 211.9) -> (216.89, 212.22)

Distance:

243.4 -> 244.62

Spacegroup:

C 2 2 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.53 4.15 1.53
Low resolution limit 41.44 41.46 1.56
Completeness 94.1 100.0 57.8
Multiplicity 6.3 7.0 2.4
I/sigma 17.5 59.2 0.5
Rmerge 0.041 0.024 2.027
CC half 1.0 1.0 0.344
Anomalous completeness 90.4 99.5 42.8
Anomalous multiplicity 3.3 3.3 3.3
Cell 56.96 65.35 124.33 90.0 90.0 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.23953

Sweep:

SWEEP2

Files:

/programs/datagrid/987/nh30_4b_01_#####.cbf

Images:

1 - 1810

Beam:

(216.89, 211.9) -> (216.89, 212.22)

Distance:

243.4 -> 244.16

Spacegroup:

C 2 2 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.48 4.02 1.48
Low resolution limit 31.57 31.58 1.51
Completeness 89.1 100.0 34.4
Multiplicity 6.1 7.2 2.2
I/sigma 6.0 36.9 0.0
Rmerge 0.069 0.042 2.072
CC half 0.999 0.999 0.27
Anomalous completeness 84.6 100.0 22.9
Anomalous multiplicity 3.3 3.3 3.3
Cell 56.869 65.287 124.225 90.0 90.0 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.