7VYR
Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody Fab fragment
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PAL/PLS BEAMLINE 11C |
Synchrotron site | PAL/PLS |
Beamline | 11C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-10-27 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.0 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 61.801, 191.676, 65.900 |
Unit cell angles | 90.00, 93.99, 90.00 |
Refinement procedure
Resolution | 47.920 - 2.200 |
R-factor | 0.1928 |
Rwork | 0.192 |
R-free | 0.23530 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4mik 7jmo |
RMSD bond length | 0.009 |
RMSD bond angle | 1.216 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX |
Refinement software | PHENIX (1.18.2_3874) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 47.920 | 2.279 |
High resolution limit [Å] | 2.200 | 2.200 |
Rmerge | 0.087 | 0.267 |
Number of reflections | 74394 | 6968 |
<I/σ(I)> | 1.36 | |
Completeness [%] | 95.4 | |
Redundancy | 6.3 | |
CC(1/2) | 0.947 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 20% (v/v) PEG 3350, 200mM NH4Cl |