X-Ray Diffraction data from Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA, source of 5NW5 structure

dataset logo thumbnail
Visualize in 3D >>

Data DOI: 10.15785/SBGRID/446 | ID: 446

Publication DOI: 10.1038/nsmb.3420

5NW5 Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Thoma Laboratory, Friedrich Miescher Institute for Biomedical Research

Release Date: 13 Jun 2017

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/446

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/446 .' (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/446 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/446 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/446 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 446 ; shasum -c files.sha'

Storage requirements: 13G

Biological Sample:

Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA

Dataset Type:

X-Ray Diffraction

Subject Composition:

DNA, Protein

Collection Facility:

Beamline PXII (X10SA), Swiss Light Source, Switzerland

Data Creation Date:

26 Feb 2014

Related Datasets:

None


Cite this Dataset

Bunker, RD; Thoma, N. 2017. "X-Ray Diffraction data for: Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA. PDB Code 5NW5", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/446.

Download Citation

Dataset Description

Three sweeps combined for final data set. Sweep 1 collected from a separate position on the crystal to subsequence sweeps. Sweeps 2 and 3 collected in inverse beam mode

Project Members

Name Additional Roles Affiliation While Working on the Project
Richard D BunkerData Collector, DepositorFriedrich Miescher Institute for Biomedical Research
Nicolas ThomaPIhttps://www.fmi.ch/research/groupleader/members/?group=118

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//446/ 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//446/ 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//446/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 0.91863

Sweep:

SWEEP3

Files:

/programs/datagrid/446/5NW5_3_#####.cbf

Images:

1 - 1800

Beam:

(146.72, 119.02) -> (146.72, 118.99)

Distance:

800.02 -> 800.5

Spacegroup:

P 21 21 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 7.18 19.4 7.18
Low resolution limit 78.03 78.03 7.31
Completeness 100.0 100.0 99.5
Multiplicity 19.0 14.1 20.9
I/sigma 7.5 25.4 0.3
Rmerge 0.277 0.089 5.126
CC half 0.996 0.997 0.6
Anomalous completeness 100.0 100.0 99.5
Anomalous multiplicity 10.5 10.5 10.5
Cell 92.16 169.719 390.151 90.0 90.0 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.