Data DOI: 10.15785/SBGRID/831 | ID: 831
7MDF Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB
Gaudet Laboratory, Harvard University
Release Date: 4 Oct 2022
1. If this dataset is locally available, it should be accessable at /programs/datagrid/831
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/831 .' (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/831 .' (Uppsala University, Sweden)
'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/831 .' (Institut Pasteur de Montevideo, Uruguay)
'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/831 .' (Shanghai Institutes for Biological Sciences, China)
3. After the transfer is completed, please issue the following command to verify data integrity:
'cd 831 ; shasum -c files.sha'
Storage requirements: 6.9G
Biological Sample:
S95A ClbP bound to acyl-D-asparagine product analog
Dataset Type:
X-Ray Diffraction
Subject Composition:
Protein
Collection Facility:
Beamline 24-ID-C, NECAT, APS, Chicago, IL
Data Creation Date:
18 Oct 2018
Related Datasets:
None
Velilla, JA; Gaudet, R. 2022. "X-Ray Diffraction data for: S95A ClbP bound to acyl-D-asparagine product analog. PDB Code 7MDF", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/831.
Bromine edge data collected from two crystals of the ClbP peptidase grown in presence of a substrate analog and in a monopalmitolein mesophase.
| Name | Additional Roles | Affiliation While Working on the Project |
|---|---|---|
| Jose A Velilla | Data Collector, Depositor | Graduate Student |
| Rachelle Gaudet | Principal Investigator | |
| Rachelle Gaudet | PI | Harvard University |
Data collected at APS beamline 24-ID-C in a Pilatus detector. Diffraction data from each crystal were separately indexed in XDS (spacegroup P 42 21 2). The two resulting .HKL files were scaled in Aimless, and the output .MTZ file was used for phasing in PHENIX with full-length ClbP (PDB:7MDE) as search model. The Rfree flags in the reflection file used for refinement were transferred from the reflection file used for refining 7MDE and extended to the full resolution range.
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.9202
Sweep:
SWEEP2
Files:
/programs/datagrid/831/RG003_16_02_1_####.cbf
Images:
1 - 450
Beam:
(217.02, 225.35) -> (217.02, 225.36)
Distance:
350.0 -> 349.62
Spacegroup:
P 42 21 2
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 2.22 | 6.02 | 2.22 |
| Low resolution limit | 51.61 | 51.63 | 2.26 |
| Completeness | 100.0 | 100.0 | 99.9 |
| Multiplicity | 15.7 | 15.6 | 10.7 |
| I/sigma | 7.9 | 32.5 | 0.5 |
| Rmerge | 0.341 | 0.061 | 5.412 |
| CC half | 0.997 | 0.999 | 0.372 |
| Anomalous completeness | 99.8 | 100.0 | 99.8 |
| Anomalous multiplicity | 8.4 | 8.4 | 8.4 |
| Cell | 96.75 | 96.75 | 183.06 | 90.0 | 90.0 | 90.0 |
|---|
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.9202
Sweep:
SWEEP2
Files:
/programs/datagrid/831/RG003_16_02_1_####.cbf
Images:
1 - 450
Beam:
(217.02, 225.35) -> (217.02, 225.36)
Distance:
350.0 -> 349.57
Spacegroup:
P 42 21 2
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 2.22 | 6.02 | 2.22 |
| Low resolution limit | 68.37 | 68.4 | 2.26 |
| Completeness | 100.0 | 100.0 | 100.0 |
| Multiplicity | 15.7 | 15.6 | 10.7 |
| I/sigma | 7.9 | 32.7 | 0.5 |
| Rmerge | 0.336 | 0.059 | 5.255 |
| CC half | 0.998 | 0.999 | 0.348 |
| Anomalous completeness | 99.9 | 100.0 | 99.7 |
| Anomalous multiplicity | 8.4 | 8.4 | 8.4 |
| Cell | 96.69 | 96.69 | 182.69 | 90.0 | 90.0 | 90.0 |
|---|
Version:
version unreported
Project:
AUTOMATIC
Crystal:
DEFAULT
Sequence Length:
0
Wavelength:
SAD - 0.9202
Sweep:
SWEEP2
Files:
/programs/datagrid/831/RG003_16_02_1_####.cbf
Images:
1 - 450
Beam:
(217.02, 225.35) -> (217.02, 225.36)
Distance:
350.0 -> 350.46
Spacegroup:
P 42 21 2
For AUTOMATIC/DEFAULT/SAD:
| ALL | LOW | HIGH | |
|---|---|---|---|
| High resolution limit | 1.94 | 5.28 | 1.94 |
| Low resolution limit | 85.16 | 85.25 | 1.98 |
| Completeness | 99.9 | 100.0 | 96.6 |
| Multiplicity | 17.3 | 16.2 | 17.9 |
| I/sigma | 6.5 | 32.1 | 0.5 |
| Rmerge | 0.395 | 0.069 | 5.735 |
| CC half | 0.999 | 1.0 | 0.418 |
| Anomalous completeness | 99.8 | 99.9 | 96.8 |
| Anomalous multiplicity | 9.2 | 9.2 | 9.2 |
| Cell | 96.312 | 96.312 | 182.355 | 90.0 | 90.0 | 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.
