7Q3Q
Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SOLEIL BEAMLINE PROXIMA 2 |
Synchrotron site | SOLEIL |
Beamline | PROXIMA 2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-10-07 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.980112 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 62.451, 62.451, 218.525 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 47.410 - 2.300 |
R-factor | 0.1866 |
Rwork | 0.185 |
R-free | 0.22020 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6ym0 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHENIX |
Refinement software | PHENIX (1.19_4092) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 47.410 | 47.410 | 2.380 |
High resolution limit [Å] | 2.300 | 8.910 | 2.300 |
Rmerge | 0.115 | 0.034 | 1.761 |
Rmeas | 0.116 | 0.034 | 1.777 |
Rpim | 0.016 | 0.005 | 0.236 |
Total number of observations | 1043029 | 17413 | 106171 |
Number of reflections | 20030 | 436 | 1923 |
<I/σ(I)> | 32.4 | 89.4 | 3.5 |
Completeness [%] | 99.4 | 99.6 | 99 |
Redundancy | 52.1 | 39.9 | 55.2 |
CC(1/2) | 1.000 | 1.000 | 0.886 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | 30% PEG 4000, 0.1 M Tris-HCl (pH 8.5) and 0.2 M Li2SO4 |