5IYY
X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04 |
Synchrotron site | Diamond |
Beamline | I04 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-02-23 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.979 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 41.525, 88.945, 41.700 |
Unit cell angles | 90.00, 91.61, 90.00 |
Refinement procedure
Resolution | 44.470 - 1.600 |
R-factor | 0.14793 |
Rwork | 0.146 |
R-free | 0.18705 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1kex |
RMSD bond length | 0.024 |
RMSD bond angle | 2.117 |
Data reduction software | xia2 |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0135) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 41.500 | 1.420 |
High resolution limit [Å] | 1.380 | 1.380 |
Rmerge | 0.137 | 0.854 |
Number of reflections | 60739 | |
<I/σ(I)> | 7.4 | 1.4 |
Completeness [%] | 98.0 | 82.5 |
Redundancy | 6.5 | 4.7 |
CC(1/2) | 0.993 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.9 | 293 | 30% w/v PEG3350, 0.2 M AmCl |