7O1N
Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
| Synchrotron site | PETRA III, EMBL c/o DESY |
| Beamline | P13 (MX1) |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2019-08-13 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9724 |
| Spacegroup name | P 32 2 1 |
| Unit cell lengths | 80.076, 80.076, 62.198 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 46.350 - 1.560 |
| R-factor | 0.1811 |
| Rwork | 0.180 |
| R-free | 0.20880 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1kex |
| RMSD bond length | 0.014 |
| RMSD bond angle | 1.965 |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER (2.7.17) |
| Refinement software | REFMAC (5.8.0266) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 46.350 | 46.300 | 1.590 |
| High resolution limit [Å] | 1.560 | 8.550 | 1.560 |
| Rmerge | 0.019 | 0.010 | 0.180 |
| Rmeas | 0.026 | 0.014 | 0.254 |
| Rpim | 0.019 | 0.010 | 0.180 |
| Total number of observations | 386 | 3145 | |
| Number of reflections | 33072 | 236 | 1619 |
| <I/σ(I)> | 17.6 | 44.2 | 3.4 |
| Completeness [%] | 100.0 | 98.9 | 100 |
| Redundancy | 1.9 | 1.6 | 1.9 |
| CC(1/2) | 0.999 | 1.000 | 0.908 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 293 | Precipitant of 20% PEG4000, 0.1M Tris (pH 8.5), 0.2M Lithium Sulfate. Protein concentration used is 10 mg/mL, mixed 1:1 with precipitant for hanging drop over reservoir of 1 mL. |
