7JJC
Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 |
| Synchrotron site | Australian Synchrotron |
| Beamline | MX1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-07-16 |
| Detector | DECTRIS EIGER2 X 9M |
| Wavelength(s) | 0.95372 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 89.930, 89.890, 108.300 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 46.383 - 2.360 |
| R-factor | 0.205604973312 |
| Rwork | 0.203 |
| R-free | 0.24994 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1kex |
| RMSD bond length | 0.003 |
| RMSD bond angle | 0.709 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER (2.5.6) |
| Refinement software | PHENIX (1.10.1) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 46.390 | 46.390 | 2.450 |
| High resolution limit [Å] | 2.360 | 8.830 | 2.360 |
| Rmerge | 0.100 | 0.020 | 1.478 |
| Rmeas | 0.108 | 0.022 | 1.584 |
| Rpim | 0.039 | 0.008 | 0.565 |
| Total number of observations | 5679 | 27837 | |
| Number of reflections | 36732 | 800 | 3656 |
| <I/σ(I)> | 11.4 | 46.7 | 1 |
| Completeness [%] | 99.6 | 99.2 | 96.2 |
| Redundancy | 7.5 | 7.1 | 7.6 |
| CC(1/2) | 0.999 | 0.999 | 0.613 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 0.1 M Sodium Citrate pH 5, 20% PEG 6K |
