8H5U
Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-021
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 | 2021-07-10 |
Detector | DECTRIS PILATUS3 S 6M |
Wavelength(s) | 0.97852 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 78.072, 104.827, 107.053 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 40.686 - 2.401 |
R-factor | 0.2262 |
Rwork | 0.225 |
R-free | 0.24510 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yz5 6b20 |
RMSD bond length | 0.004 |
RMSD bond angle | 0.725 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHASER |
Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.490 |
High resolution limit [Å] | 2.400 | 2.400 |
Rmerge | 0.173 | 0.722 |
Number of reflections | 33895 | 3240 |
<I/σ(I)> | 25.692 | |
Completeness [%] | 97.9 | |
Redundancy | 11.9 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 18% w/v polyethylene glycol 20000 |