8H5T
Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-015
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRF BEAMLINE BL19U1 |
| Synchrotron site | SSRF |
| Beamline | BL19U1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-10-17 |
| Detector | DECTRIS PILATUS3 S 6M |
| Wavelength(s) | 0.97852 |
| Spacegroup name | I 41 |
| Unit cell lengths | 75.816, 75.816, 119.834 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 26.152 - 2.000 |
| R-factor | 0.1727 |
| Rwork | 0.171 |
| R-free | 0.20470 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 6yz5 5tp3 |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.850 |
| Data reduction software | HKL-3000 |
| Data scaling software | HKL-3000 |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.070 |
| High resolution limit [Å] | 2.000 | 2.000 |
| Rmerge | 0.110 | 0.664 |
| Number of reflections | 22938 | 2299 |
| <I/σ(I)> | 46.136 | |
| Completeness [%] | 100.0 | |
| Redundancy | 13.2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.2 M sodium formate, pH 7.2, 20% w/v polyethylene glycol 3350 |
