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/220 | ID: 220

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/220

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/220 .' (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/220 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/220 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/220 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 220 ; shasum -c files.sha'

Storage requirements: 8.4G

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:

219


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/220.

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Dataset Description

SeMet dataset.

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 mosflm_beam_centre=216.6,220.53 /programs/datagrid//220/ 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 mosflm_beam_centre=216.6,220.53 /programs/datagrid//220/ 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 mosflm_beam_centre=216.6,220.53 /programs/datagrid//220/ 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/220/TgC1Se_1_13_2_####.cbf

Images:

1 - 720

Beam:

(216.6, 220.53) -> (216.6, 220.54)

Distance:

650.0 -> 655.14

Spacegroup:

P 1 21 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 3.31 8.99 3.31
Low resolution limit 102.13 102.17 3.37
Completeness 99.3 100.0 93.7
Multiplicity 13.6 13.4 13.8
I/sigma 3.9 29.1 0.3
Rmerge 0.474 0.085 7.536
CC half 0.993 0.997 0.388
Anomalous completeness 98.8 99.6 93.1
Anomalous multiplicity 7.0 7.0 7.0
Cell 77.318 91.752 107.587 90.0 108.333 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.