X-Ray Diffraction data from LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide, source of 8FFE structure

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Data DOI: 10.15785/SBGRID/975 | ID: 975

8FFE Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Garcia Laboratory, Stanford University

Release Date: 3 Mar 2023

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/975

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/975 .' (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/975 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/975 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/975 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 975 ; shasum -c files.sha'

Storage requirements: 8.4G

Biological Sample:

LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

beamline 2.0.1, ALS

Data Creation Date:

11 Nov 2022

Related Datasets:

976


Cite this Dataset

Jude, KM; Garcia, KC; Garcia, K. 2023. "X-Ray Diffraction data for: LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide. PDB Code 8FFE", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/975.

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Dataset Description

Native dataset collected from two crystals

Project Members

Name Additional Roles Affiliation While Working on the Project
Kevin M JudeData Collector, DepositorHHMI, Stanford University
K C GarciaHHMI/Stanford University
K. Christopher GarciaPIStanford University

Reprocessing Instructions

Data were processed with XDS. 1447_Pin1_0_?????.cbf used frames 1-360. 1447_Pin2_0_?????.cbf used frames 1-720

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//975/ 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//975/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.03895

Sweep:

SWEEP2

Files:

/programs/datagrid/975/1447_Pin2_0_#####.cbf

Images:

1 - 720

Beam:

(218.44, 203.13) -> (218.44, 203.89)

Distance:

300.0 -> 299.61

Spacegroup:

C 1 2 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.76 7.48 2.76
Low resolution limit 47.26 47.27 2.81
Completeness 99.6 99.3 99.2
Multiplicity 5.4 6.1 3.4
I/sigma 4.3 10.5 1.0
Rmerge 0.414 0.163 1.198
CC half 0.846 0.949 0.284
Anomalous completeness 94.3 97.4 88.7
Anomalous multiplicity 2.8 2.8 2.8
Cell 124.86 91.13 103.31 90.0 103.57 90.0
/programs/x86_64-linux/dials/3.12.0/bin.capsules//xia2 pipeline=dials /programs/datagrid//975/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.


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.