6TDB
Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2016-01-23 |
Detector | DECTRIS PILATUS3 S 6M |
Wavelength(s) | 0.977 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 107.359, 140.122, 74.357 |
Unit cell angles | 90.00, 132.97, 90.00 |
Refinement procedure
Resolution | 70.060 - 2.450 |
R-factor | 0.1859 |
Rwork | 0.183 |
R-free | 0.24970 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4rn5 |
RMSD bond length | 0.004 |
RMSD bond angle | 0.691 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (1.14_3260) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 70.060 | 70.060 | 2.580 |
High resolution limit [Å] | 2.450 | 7.750 | 2.450 |
Number of reflections | 29170 | 928 | 4278 |
<I/σ(I)> | 10.6 | ||
Completeness [%] | 98.9 | ||
Redundancy | 3.4 | ||
CC(1/2) | 0.996 | 0.997 | 0.738 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 293 | N2b1-apo 0.05 M KCl, 0.01 M MgCl2 and 15 % (w/v) PEG600 N2b1/VEGFB167 0.1 M HEPES pH 7.5, 10 % (w/v) PEG4000, 20 % (w/v) isopropanol |