X-Ray Diffraction data from CDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7 , source of 4YGA structure

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Data DOI: 10.15785/SBGRID/219 | ID: 219

Publication DOI: 10.1073/pnas.1505914112

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

Schwartz Laboratory, Massachusetts Institute of Technology

Release Date: 15 Jan 2016

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/219

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/219 .' (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/219 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/219 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/219 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 219 ; shasum -c files.sha'

Storage requirements: 4.7G

Biological Sample:

CDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7

Dataset Type:

X-Ray Diffraction

Subject Composition:

Ligand, Protein

Collection Facility:

beamline 24-ID-C, NE-CAT, APS, Chicago, IL

Data Creation Date:

14 Dec 2013

Related Datasets:

220


Cite this Dataset

Knockenhauer, KE; Schwartz, T. 2016. "X-Ray Diffraction data for: CDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7 . PDB Code 4YGA", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/219.

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Dataset Description

Native data.

Project Members

Name Additional Roles Affiliation While Working on the Project
Kevin E KnockenhauerData Collector, DepositorMassachusetts Institute of Technology
Thomas SchwartzPIMassachusetts Institute of Technology

Reprocessing Instructions

none

Reprocessing Data

About Reprocessing

xia2 -2d

xia2 -3d

xia2 -3dii

xia2 -dials
/programs/x86_64-linux/dials/3.12.0/bin.capsules//xia2 pipeline=3d /programs/datagrid//219/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/3.12.0/bin.capsules//xia2 pipeline=3dii /programs/datagrid//219/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/3.12.0/bin.capsules//xia2 pipeline=dials /programs/datagrid//219/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.9792

Sweep:

SWEEP2

Files:

/programs/datagrid/219/TgC1_5_12_2_####.cbf

Images:

1 - 400

Beam:

(216.6, 220.62) -> (216.6, 220.66)

Distance:

600.0 -> 603.35

Spacegroup:

P 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.56 6.94 2.56
Low resolution limit 100.94 101.02 2.6
Completeness 85.7 92.4 46.1
Multiplicity 4.0 4.1 3.7
I/sigma 5.6 36.6 0.1
Rmerge 0.103 0.044 2.683
CC half 0.993 0.991 0.429
Anomalous completeness 78.5 86.8 36.8
Anomalous multiplicity 2.1 2.1 2.1
Cell 76.837 90.968 106.332 88.619 71.729 89.621

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.