7JVB
Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 23-ID-B |
Synchrotron site | APS |
Beamline | 23-ID-B |
Temperature [K] | 80 |
Detector technology | PIXEL |
Collection date | 2020-08-07 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 70.716, 70.716, 435.037 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 38.959 - 3.287 |
R-factor | 0.2834 |
Rwork | 0.281 |
R-free | 0.32220 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6waq |
RMSD bond length | 0.005 |
RMSD bond angle | 1.663 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 38.960 | 3.405 |
High resolution limit [Å] | 3.287 | 3.287 |
Rmerge | 0.156 | 0.591 |
Rpim | 0.108 | 0.445 |
Number of reflections | 17442 | 1391 |
<I/σ(I)> | 7.8 | |
Completeness [%] | 96.3 | |
Redundancy | 6.2 | |
CC(1/2) | 1.000 | 0.811 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | 100 mM sodium cacodylate pH 6.5, 1 M sodium citrate |