X-Ray Diffraction data from CD47 ectodomain with diabody 5F9, source of 5IWL structure

Data DOI: 10.15785/SBGRID/340 | ID: 340

Publication DOI: 10.1172/JCI81603

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

Garcia Laboratory, Stanford University

Release Date: Aug. 2, 2016

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/340

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/340 .' (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/340 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/340 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/340 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 340 ; shasum -c files.sha'

Storage requirements: 3.2G

Biological Sample:

CD47 ectodomain with diabody 5F9

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

beamline 7-1, SSRL, Stanford, CA

Data Creation Date:

April 3, 2015

Related Datasets:

None


Cite this Dataset

Jude, KM; Wu, D; Garcia, K. 2016. "X-Ray Diffraction data for: CD47 ectodomain with diabody 5F9. PDB Code 5IWL", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/340.

Download Citation

Dataset Description

native dataset

Project Members

Name Additional Roles Affiliation While Working on the Project
Kevin M JudeDepositorStanford University
Di WuData CollectorStanford University
K. Christopher GarciaPIStanford University

Reprocessing Instructions

processed with HKL2000

Reprocessing Data

About Reprocessing

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12708

Sweep:

SWEEP2

Files:

/programs/datagrid/340/5F9B8_1_#####.img

Images:

1 - 90

Beam:

(157.5, 157.5) -> (157.5, 157.47)

Distance:

350.0 -> 350.27

Spacegroup:

P 3 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.89 7.84 2.89
Low resolution limit 89.35 89.39 2.94
Completeness 95.6 90.2 98.0
Multiplicity 10.8 10.7 8.6
I/sigma 12.3 37.4 1.4
Rmerge 0.199 0.039 1.502
CC half 0.993 0.999 0.352
Anomalous completeness 94.6 94.6 96.7
Anomalous multiplicity 5.8 5.8 5.8
Cell 103.17 103.17 65.506 90.0 90.0 120.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12708

Sweep:

SWEEP2

Files:

/programs/datagrid/340/5F9B8_1_#####.img

Images:

1 - 90

Beam:

(157.5, 157.5) -> (157.5, 157.35)

Distance:

350.0 -> 349.69

Spacegroup:

P 3 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.88 7.81 2.88
Low resolution limit 52.85 52.86 2.93
Completeness 95.7 89.6 97.4
Multiplicity 8.8 11.0 5.7
I/sigma 10.4 34.7 1.1
Rmerge 0.179 0.045 1.491
CC half 0.992 1.0 0.299
Anomalous completeness 96.6 94.5 97.6
Anomalous multiplicity 4.7 4.7 4.7
Cell 103.21 103.21 131.08 90.0 90.0 120.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12708

Sweep:

SWEEP2

Files:

/programs/datagrid/340/5F9B8_1_#####.img

Images:

1 - 90

Beam:

(157.5, 157.5) -> (157.5, 157.35)

Distance:

350.0 -> 349.78

Spacegroup:

P 3 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.87 7.78 2.87
Low resolution limit 52.85 52.86 2.92
Completeness 95.7 89.6 97.2
Multiplicity 11.2 11.1 8.0
I/sigma 10.6 33.7 1.2
Rmerge 0.225 0.045 1.627
CC half 0.995 1.0 0.372
Anomalous completeness 96.8 94.6 97.3
Anomalous multiplicity 5.9 5.9 5.9
Cell 103.21 103.21 131.08 90.0 90.0 120.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12708

Sweep:

SWEEP2

Files:

/programs/datagrid/340/5F9B8_1_#####.img

Images:

1 - 90

Beam:

(157.5, 157.5) -> (157.5, 157.33)

Distance:

350.0 -> 349.48

Spacegroup:

P 3 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.84 7.7 2.84
Low resolution limit 51.52 51.53 2.89
Completeness 95.8 90.0 98.9
Multiplicity 11.1 11.0 9.0
I/sigma 12.5 35.6 1.3
Rmerge 0.157 0.038 1.501
CC half 0.996 0.999 0.498
Anomalous completeness 96.3 95.6 98.6
Anomalous multiplicity 5.9 5.9 5.9
Cell 103.045 103.045 65.436 90.0 90.0 120.0

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.