7W1S
Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-007
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL18U1 |
Synchrotron site | SSRF |
Beamline | BL18U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-05-17 |
Detector | DECTRIS PILATUS3 S 6M |
Wavelength(s) | 0.97915 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 56.804, 56.804, 219.773 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.651 - 1.997 |
R-factor | 0.1999 |
Rwork | 0.199 |
R-free | 0.22390 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yz5 6b20 |
RMSD bond length | 0.003 |
RMSD bond angle | 0.542 |
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] | 1.997 | 2.000 |
Rmerge | 0.182 | 0.739 |
Number of reflections | 25547 | 2451 |
<I/σ(I)> | 16.5 | |
Completeness [%] | 99.9 | |
Redundancy | 17.4 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.2 M Sodium chloride, 20% w/v Polyethylene glycol 3350, pH 6.9 |