8CWV
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 23-ID-D |
Synchrotron site | APS |
Beamline | 23-ID-D |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-10-31 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.03320 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 89.310, 142.024, 149.367 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 42.780 - 2.510 |
R-factor | 0.239 |
Rwork | 0.238 |
R-free | 0.26400 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7JMW; 7KN5 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHASER |
Refinement software | PHENIX (1.19.2_4158) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.540 |
High resolution limit [Å] | 2.500 | 6.780 | 2.500 |
Rmerge | 0.147 | 0.088 | 1.120 |
Rmeas | 0.173 | 0.102 | 1.332 |
Rpim | 0.088 | 0.050 | 0.700 |
Total number of observations | 90065 | ||
Number of reflections | 27562 | 1513 | 1344 |
<I/σ(I)> | 4.3 | ||
Completeness [%] | 84.0 | 85.5 | 81.9 |
Redundancy | 3.3 | 3.7 | 3.1 |
CC(1/2) | 0.978 | 0.459 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 40% MPD, 0.1M cacodylate pH 6.5 5% (w/v) PEG-8000, final pH 7.0 |