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X-Ray Diffraction data from Mouse surfactant protein B, wild-type N-terminal domain with bound lipid, source of 6VYN structure

Data DOI: 10.15785/SBGRID/763 | ID: 763

Publication DOI: 10.1016/j.molcel.2020.10.042

6VYN Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Rapoport Laboratory, Harvard Medical School

Release Date: Nov. 17, 2020

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/763

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/763 .' (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/763 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/763 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/763 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 763 ; shasum -c files.sha'

Storage requirements: 3.1G

Biological Sample:

Mouse surfactant protein B, wild-type N-terminal domain with bound lipid

Dataset Type:

X-Ray Diffraction

Subject Composition:

Ligand, Protein

Collection Facility:

APS 24-ID-C

Data Creation Date:

Oct. 18, 2017

Related Datasets:

762, 761, 760, 759, 758, 757


Cite this Dataset

Bodnar, NO; Rapoport, TA. 2020. "X-Ray Diffraction data for: Mouse surfactant protein B, wild-type N-terminal domain with bound lipid. PDB Code 6VYN", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/763.

Download Citation

Dataset Description

Sulfur-SAD dataset #7 (of 7 that were merged to create a dataset for structure solution)

Project Members

Name Additional Roles Affiliation While Working on the Project
Nicholas O BodnarData Collector, DepositorHMS
Tom A RapoportHMS
Tom RapoportPIHarvard Medical School

Reprocessing Instructions

Datasets 1-7 were indexed/integrated with XDS, then combined using the Phenix scale_and_merge program

Reprocessing Data

About Reprocessing

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.7712

Sweep:

SWEEP1

Files:

/programs/datagrid/763/puck1_sample4_1_1_####.cbf

Images:

1 - 520

Beam:

(217.0, 223.04) -> (217.0, 222.93)

Distance:

215.0 -> 215.26

Spacegroup:

P 1 21 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.44 6.62 2.44
Low resolution limit 60.59 60.61 2.48
Completeness 90.6 90.3 90.4
Multiplicity 2.6 2.6 2.6
I/sigma 9.0 23.3 0.5
Rmerge 0.046 0.025 1.661
CC half 0.989 0.984 0.319
Anomalous completeness 59.4 73.3 54.3
Anomalous multiplicity 1.6 1.6 1.6
Cell 108.32 94.34 114.92 90.0 90.34 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.7712

Sweep:

SWEEP1

Files:

/programs/datagrid/763/puck1_sample4_1_1_####.cbf

Images:

1 - 520

Beam:

(217.0, 223.04) -> (217.0, 222.95)

Distance:

215.0 -> 214.98

Spacegroup:

P 1 21 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.43 6.59 2.43
Low resolution limit 79.06 79.1 2.47
Completeness 90.6 90.4 90.3
Multiplicity 2.6 2.6 2.6
I/sigma 8.9 23.2 0.5
Rmerge 0.046 0.025 1.735
CC half 0.989 0.984 0.297
Anomalous completeness 59.4 73.3 54.3
Anomalous multiplicity 1.6 1.6 1.6
Cell 108.32 94.34 114.92 90.0 90.34 90.0

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.7712

Sweep:

SWEEP1

Files:

/programs/datagrid/763/puck1_sample4_1_1_####.cbf

Images:

1 - 520

Beam:

(217.0, 223.04) -> (217.0, 222.93)

Distance:

215.0 -> 215.64

Spacegroup:

P 21 21 21

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.28 6.18 2.28
Low resolution limit 114.99 115.14 2.32
Completeness 98.6 98.8 94.8
Multiplicity 4.6 4.6 4.2
I/sigma 5.7 34.3 0.0
Rmerge 0.092 0.041 2.381
CC half 0.993 0.991 0.405
Anomalous completeness 95.4 96.3 88.1
Anomalous multiplicity 2.5 2.5 2.5
Cell 94.455 108.452 114.989 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.