5JGQ
X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 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 | 2015-07-30 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.979 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 40.789, 89.568, 41.385 |
Unit cell angles | 90.00, 98.57, 90.00 |
Refinement procedure
Resolution | 44.780 - 1.600 |
R-factor | 0.16219 |
Rwork | 0.161 |
R-free | 0.19304 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1kex |
RMSD bond length | 0.020 |
RMSD bond angle | 1.864 |
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] | 40.920 | 1.630 |
High resolution limit [Å] | 1.600 | 1.600 |
Rmerge | 0.047 | 0.442 |
Number of reflections | 37578 | |
<I/σ(I)> | 10.5 | 2 |
Completeness [%] | 97.0 | 75.3 |
Redundancy | 3.1 | 1.9 |
CC(1/2) | 0.998 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.9 | 289 | 18%PEG3350+0.2M NH4Cl |