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X-Ray Diffraction data from Cyclophilin A, source of 4YUO structure

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Data DOI: 10.15785/SBGRID/68 | ID: 68

Publication DOI: 10.1101/016733

4YUO Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Fraser Laboratory, University of California, San Francisco

Release Date: May 8, 2015

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/68

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/68 .' (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/68 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/68 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/68 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 68 ; shasum -c files.sha'

Storage requirements: 2.1G

Biological Sample:

Cyclophilin A

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

SSRL beamline 11-1

Data Creation Date:

June 25, 2013

Related Datasets:

None


Cite this Dataset

Fraser, JS. 2015. "X-Ray Diffraction data for: Cyclophilin A. PDB Code 4YUO", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/68.

Download Citation

Dataset Description

Highest resolution room temperature diffraction data set for Cyclophilin A. Collected under paratone oil.

Project Members

Name Additional Roles Affiliation While Working on the Project
James S FraserData Collector, DepositorUniversity of California San Francisco
James FraserPIUniversity of California, San Francisco

Reprocessing Instructions

360 images processed in XDS to 1.2 A resolution. This dataset should process fine with all automated data processing pipelines.

Reprocessing Data

About Reprocessing

xia2 -2d

xia2 -3d

xia2 -3dii

xia2 -dials
/programs/x86_64-linux/dials/1.11.4/dials-1.11.4/build/bin/xia2 pipeline=2d /programs/datagrid//68/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/1.11.4/dials-1.11.4/build/bin/xia2 pipeline=3d /programs/datagrid//68/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97945

Sweep:

SWEEP1

Files:

/programs/datagrid/68/set_1_1_#####.cbf

Images:

1 - 360

Beam:

(217.32, 211.82) -> (217.32, 211.53)

Distance:

183.02 -> 182.37

Spacegroup:

P 21 21 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.11 3.01 1.11
Low resolution limit 26.63 26.64 1.13
Completeness 92.7 97.7 61.2
Multiplicity 5.8 6.4 4.5
I/sigma 7.9 15.1 1.1
Rmerge 0.106 0.105 1.048
CC half 0.989 0.981 0.45
Anomalous completeness 86.2 96.9 50.5
Anomalous multiplicity 3.1 3.1 3.1
Cell 42.92 52.44 89.14 90.0 90.0 90.0
/programs/x86_64-linux/dials/1.11.4/dials-1.11.4/build/bin/xia2 pipeline=3dii /programs/datagrid//68/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97945

Sweep:

SWEEP1

Files:

/programs/datagrid/68/set_1_1_#####.cbf

Images:

1 - 360

Beam:

(217.32, 211.82) -> (217.32, 211.56)

Distance:

183.02 -> 182.36

Spacegroup:

P 21 21 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.12 3.04 1.12
Low resolution limit 44.57 44.61 1.14
Completeness 93.9 97.7 66.9
Multiplicity 6.0 6.4 4.8
I/sigma 7.9 15.2 1.1
Rmerge 0.106 0.105 1.125
CC half 0.988 0.981 0.471
Anomalous completeness 88.6 96.8 57.6
Anomalous multiplicity 3.2 3.2 3.2
Cell 42.92 52.44 89.14 90.0 90.0 90.0
/programs/x86_64-linux/dials/1.11.4/dials-1.11.4/build/bin/xia2 pipeline=dials /programs/datagrid//68/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.97945

Sweep:

SWEEP1

Files:

/programs/datagrid/68/set_1_1_#####.cbf

Images:

1 - 360

Beam:

(217.32, 211.82) -> (217.32, 211.54)

Distance:

183.02 -> 181.83

Spacegroup:

P 1 21 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 1.23 3.33 1.23
Low resolution limit 45.03 45.06 1.25
Completeness 90.8 89.6 78.6
Multiplicity 3.5 3.7 3.3
I/sigma 2.7 5.2 0.8
Rmerge 0.358 0.321 1.868
CC half 0.693 0.577 0.281
Anomalous completeness 83.2 87.4 67.9
Anomalous multiplicity 1.8 1.8 1.8
Cell 42.881 89.071 52.188 90.0 90.108 90.0
This dataset is part of the SBDB Pilot Reference Collection, and has processed intensities available from that collection.

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.