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X-Ray Diffraction data from neurexin 1alpha extracellular domain, source of 3QCW structure

Data DOI: 10.15785/SBGRID/78 | ID: 78

Publication DOI: 10.1016/j.str.2011.03.012

3QCW Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Rudenko Laboratory, University of Texas Medical Branch

Release Date: May 11, 2015

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/78

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/78 .' (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/78 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/78 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/78 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 78 ; shasum -c files.sha'

Storage requirements: 20G

Biological Sample:

neurexin 1alpha extracellular domain

Dataset Type:

X-Ray Diffraction

Subject Composition:

Protein

Collection Facility:

APS (Chicago, IL) beam-line LS-CAT 21-ID-D

Data Creation Date:

June 12, 2010

Related Datasets:

218


Cite this Dataset

Rudenko, G. 2015. "X-Ray Diffraction data for: neurexin 1alpha extracellular domain. PDB Code 3QCW", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/78.

Download Citation

Dataset Description

native high resolution data set used for final refinement of structure 3QCW; 5 wedges of 125 frames each, 0.5 degree oscillation angle; collected at 1.12718 Ang (10 999.5 eV); XD 300 mm MarMosaic CCD 300 detector; beam position (x: 150.0 mm , y: 150.0 mm)

Project Members

Name Additional Roles Affiliation While Working on the Project
Gabrielle RudenkoData Collector, DepositorUTMB
Gabrielle RudenkoPIUniversity of Texas Medical Branch

Reprocessing Instructions

data processed with HKL2000 (50 - 2.65 Ang, space group P1). Integration: use 'overlap spot' command; Scaling: use 'non-slipping crystal, imperfect goniostat'; absorption correction high commands; Convert data from Is to Fs and Truncate using CCP4.

Reprocessing Data

About Reprocessing

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12718

Sweep:

SWEEP5

Files:

/programs/datagrid/78/n190q_012_0.###

Images:

1 - 125

Beam:

(150.0, 150.0) -> (150.0, 150.05)

Distance:

300.0 -> 299.97

Spacegroup:

P 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.37 6.43 2.37
Low resolution limit 93.67 93.74 2.41
Completeness 90.4 98.8 36.9
Multiplicity 3.1 3.4 1.2
I/sigma 6.1 11.9 1.0
Rmerge 0.098 0.047 0.0
CC half 0.993 0.995 0.591
Anomalous completeness 82.4 97.6 9.1
Anomalous multiplicity 1.6 1.6 1.6
Cell 60.976 114.824 160.163 90.49 90.527 92.114

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12718

Sweep:

SWEEP5

Files:

/programs/datagrid/78/n190q_012_0.###

Images:

1 - 125

Beam:

(150.0, 150.0) -> (150.0, 149.93)

Distance:

300.0 -> 299.61

Spacegroup:

P 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.45 6.64 2.45
Low resolution limit 48.34 48.35 2.49
Completeness 92.5 98.8 52.7
Multiplicity 3.1 3.4 1.3
I/sigma 7.6 17.9 0.9
Rmerge 0.076 0.039 0.511
CC half 0.991 0.986 0.392
Anomalous completeness 84.1 96.3 14.6
Anomalous multiplicity 1.6 1.6 1.6
Cell 61.06 115.01 160.47 90.45 90.54 92.11

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12718

Sweep:

SWEEP5

Files:

/programs/datagrid/78/n190q_012_0.###

Images:

1 - 125

Beam:

(150.0, 150.0) -> (150.0, 149.92)

Distance:

300.0 -> 299.79

Spacegroup:

P 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.46 6.67 2.46
Low resolution limit 57.46 57.48 2.5
Completeness 92.7 98.7 52.3
Multiplicity 3.1 3.4 1.3
I/sigma 7.7 17.9 0.9
Rmerge 0.076 0.039 0.562
CC half 0.99 0.983 0.391
Anomalous completeness 84.7 96.1 14.6
Anomalous multiplicity 1.6 1.6 1.6
Cell 61.06 115.01 160.46 90.45 90.54 92.11

Version:

version unreported

Project:

AUTOMATIC

Crystal:

DEFAULT

Sequence Length:

0

Wavelength:

SAD - 1.12718

Sweep:

SWEEP5

Files:

/programs/datagrid/78/n190q_012_0.###

Images:

1 - 125

Beam:

(150.0, 150.0) -> (150.0, 150.01)

Distance:

300.0 -> 299.83

Spacegroup:

P 1

For AUTOMATIC/DEFAULT/SAD:

ALL LOW HIGH
High resolution limit 2.4 6.5 2.4
Low resolution limit 65.73 65.75 2.44
Completeness 92.4 98.9 37.8
Multiplicity 3.1 3.4 1.2
I/sigma 5.8 11.4 1.0
Rmerge 0.089 0.042 0.0
CC half 0.994 0.996 0.626
Anomalous completeness 84.3 97.6 9.3
Anomalous multiplicity 1.6 1.6 1.6
Cell 61.122 115.159 160.771 90.301 90.472 92.146
This dataset is part of the SBDB Pilot Reference Collection, and has processed intensities available from that collection.

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.