Limited Operations 2024/02/27 7AM ET - 10AM ET

The SBDB will be operating at a reduced level between 7AM and 10AM 2024/02/27 due to underlying system maintance. New dataset registrations, dataset depositions, downloads of published datasets from HMS, deposition credential requests, and other inquiries will be unavailable during this maintance.

X-Ray Diffraction data from S95A ClbP bound to monoolein, source of 7MDE structure

Data DOI: 10.15785/SBGRID/833 | ID: 833

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

Gaudet Laboratory, Harvard University

Release Date: Oct. 4, 2022

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/833

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/833 .' (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/833 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/833 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/833 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 833 ; shasum -c files.sha'

Storage requirements: 2.7G

Biological Sample:

S95A ClbP bound to monoolein

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

Beamline 24-ID-C, NECAT, APS, Chicago, IL

Data Creation Date:

June 13, 2018

Related Datasets:

None


Cite this Dataset

Velilla, JA; Gaudet, R. 2022. "X-Ray Diffraction data for: S95A ClbP bound to monoolein. PDB Code 7MDE", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/833.

Download Citation

Dataset Description

Data collected at the selenium edge of a single crystal of selenomethionine-substituted ClbP grown in a monoolein mesophase.

Project Members

Name Additional Roles Affiliation While Working on the Project
Jose A VelillaData Collector, DepositorGraduate Student
Rachelle GaudetPrincipal Investigator
Rachelle GaudetPIHarvard University

Reprocessing Instructions

Data collected at APS beamline 24-ID-C in a Pilatus detector. Diffraction data from a single crystal were indexed in XDS (spacegroup P 42 21 2). The resulting .HKL file was scaled in Aimless, and the output .MTZ file was used for phasing in PHENIX with the periplasmic domain structure (PDB: 3O3V) as search model. The Rfree flags in the reflection file were generated randomly.

Reprocessing Data

About Reprocessing

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.9792

Sweep:

SWEEP1

Files:

/programs/datagrid/833/RG003_04_01_1_####.cbf

Images:

1 - 450

Beam:

(216.6, 223.02) -> (216.6, 222.89)

Distance:

350.0 -> 352.79

Spacegroup:

C 2 2 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.66 7.22 2.66
Low resolution limit 61.31 61.33 2.71
Completeness 78.4 72.4 81.1
Multiplicity 4.3 4.3 4.3
I/sigma 5.6 22.8 0.5
Rmerge 0.195 0.038 1.715
CC half 0.986 0.997 0.311
Anomalous completeness 68.0 65.0 71.6
Anomalous multiplicity 2.4 2.4 2.4
Cell 136.98 137.33 183.93 90.0 90.0 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.9792

Sweep:

SWEEP1

Files:

/programs/datagrid/833/RG003_04_01_1_####.cbf

Images:

1 - 450

Beam:

(216.6, 223.02) -> (216.6, 222.9)

Distance:

350.0 -> 351.41

Spacegroup:

C 2 2 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.67 7.25 2.67
Low resolution limit 96.99 97.06 2.72
Completeness 78.4 72.4 81.1
Multiplicity 4.3 4.3 4.4
I/sigma 5.7 22.6 0.5
Rmerge 0.192 0.038 1.768
CC half 0.992 0.999 0.367
Anomalous completeness 67.9 65.5 71.8
Anomalous multiplicity 2.4 2.4 2.4
Cell 137.0 137.34 183.94 90.0 90.0 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.9792

Sweep:

SWEEP1

Files:

/programs/datagrid/833/RG003_04_01_1_####.cbf

Images:

1 - 450

Beam:

(216.6, 223.02) -> (216.6, 222.9)

Distance:

350.0 -> 351.92

Spacegroup:

P 42 21 2

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.24 6.08 2.24
Low resolution limit 97.19 97.28 2.28
Completeness 100.0 100.0 99.5
Multiplicity 6.5 6.0 6.7
I/sigma 4.8 26.3 0.3
Rmerge 0.279 0.057 3.064
CC half 0.993 0.998 0.339
Anomalous completeness 99.8 99.8 99.2
Anomalous multiplicity 3.5 3.5 3.5
Cell 97.19 97.19 184.142 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.