X-Ray Diffraction data from Bacteroides fragilis fragipain protease, source of 5DYN structure

Data DOI: 10.15785/SBGRID/225 | ID: 225

Publication DOI: 10.1038/nm.4077

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

Crosson Laboratory, University of Chicago

Release Date: March 8, 2016

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/225

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/225 .' (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/225 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/225 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/225 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 225 ; shasum -c files.sha'

Storage requirements: 3.2G

Biological Sample:

Bacteroides fragilis fragipain protease

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

LS-CAT, 21-ID-F. Advanced Photon Source.

Data Creation Date:

Feb. 2, 2014

Related Datasets:

None


Cite this Dataset

Bubeck Wardenburg, J; Choi, V; Herrou, J; Crosson, S. 2016. "X-Ray Diffraction data for: Bacteroides fragilis fragipain protease. PDB Code 5DYN", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/225.

Download Citation

Dataset Description

native dataset collected from single crystal of B. fragilis fragipain protease

Project Members

Name Additional Roles Affiliation While Working on the Project
Juliane Bubeck WardenburgUniversity of Chicago
Vivian ChoiData CollectorUniversity of Chicago
Julien HerrouData CollectorUniversity of Chicago
Sean CrossonData Collector, Depositor, PIUniversity of Chicago

Reprocessing Instructions

data were indexed in P21212 to 2.48 Angstrom using xia2 -3d

Reprocessing Data

About Reprocessing

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97872

Sweep:

SWEEP1

Files:

/programs/datagrid/225/Viv2_2.###

Images:

1 - 180

Beam:

(112.38, 111.95) -> (112.38, 112.03)

Distance:

200.0 -> 200.07

Spacegroup:

P 21 21 2

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.23 6.05 2.23
Low resolution limit 62.29 62.32 2.27
Completeness 100.0 100.0 100.0
Multiplicity 6.8 6.1 7.0
I/sigma 6.7 17.1 1.1
Rmerge 0.212 0.062 1.608
CC half 0.986 0.971 0.319
Anomalous completeness 99.9 99.9 100.0
Anomalous multiplicity 3.7 3.7 3.7
Cell 124.589 49.005 61.023 90.0 90.0 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97872

Sweep:

SWEEP1

Files:

/programs/datagrid/225/Viv2_2.###

Images:

1 - 180

Beam:

(112.38, 111.95) -> (112.38, 111.93)

Distance:

200.0 -> 199.08

Spacegroup:

P 21 21 2

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.25 6.1 2.25
Low resolution limit 41.43 41.44 2.29
Completeness 100.0 100.0 100.0
Multiplicity 7.2 6.4 7.4
I/sigma 10.8 34.7 1.3
Rmerge 0.144 0.038 1.602
CC half 0.998 0.999 0.414
Anomalous completeness 99.8 99.6 99.8
Anomalous multiplicity 3.9 3.9 3.9
Cell 124.29 48.89 60.86 90.0 90.0 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97872

Sweep:

SWEEP1

Files:

/programs/datagrid/225/Viv2_2.###

Images:

1 - 180

Beam:

(112.38, 111.95) -> (112.38, 111.93)

Distance:

200.0 -> 199.33

Spacegroup:

P 21 21 2

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.23 6.05 2.23
Low resolution limit 60.86 60.88 2.27
Completeness 100.0 100.0 100.0
Multiplicity 7.2 6.4 7.4
I/sigma 10.6 34.2 1.2
Rmerge 0.149 0.038 1.696
CC half 0.998 0.999 0.398
Anomalous completeness 99.8 99.6 99.9
Anomalous multiplicity 3.9 3.9 3.9
Cell 124.29 48.89 60.86 90.0 90.0 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97872

Sweep:

SWEEP1

Files:

/programs/datagrid/225/Viv2_2.###

Images:

1 - 180

Beam:

(112.38, 111.95) -> (112.38, 111.99)

Distance:

200.0 -> 199.41

Spacegroup:

P 21 21 2

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.26 6.14 2.26
Low resolution limit 62.06 62.08 2.3
Completeness 100.0 100.0 98.2
Multiplicity 7.1 6.2 7.2
I/sigma 5.6 11.9 1.1
Rmerge 0.184 0.063 1.875
CC half 0.983 0.968 0.635
Anomalous completeness 99.9 99.9 98.1
Anomalous multiplicity 3.8 3.8 3.8
Cell 124.122 48.834 60.79 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.