8RJ7
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | ALBA BEAMLINE XALOC |
| Synchrotron site | ALBA |
| Beamline | XALOC |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-09-24 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.97926 |
| Spacegroup name | P 32 |
| Unit cell lengths | 89.164, 89.164, 200.247 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 43.520 - 2.100 |
| R-factor | 0.1831 |
| Rwork | 0.181 |
| R-free | 0.22150 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.852 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 44.580 | 2.140 |
| High resolution limit [Å] | 2.100 | 2.100 |
| Rmerge | 0.079 | 0.749 |
| Rpim | 0.090 | 0.885 |
| Number of reflections | 103348 | 5173 |
| <I/σ(I)> | 8.4 | 1.6 |
| Completeness [%] | 99.4 | 99.8 |
| Redundancy | 4.1 | 3.6 |
| CC(1/2) | 0.997 | 0.560 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 15% PEG-3350, 100mM Bicine pH 9, 20 mM (NH4)2SO4 |
