6ZCZ
Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-05-01 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97625 |
Spacegroup name | H 3 |
Unit cell lengths | 177.867, 177.867, 87.715 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 35.260 - 2.650 |
R-factor | 0.2167 |
Rwork | 0.215 |
R-free | 0.25950 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yla |
RMSD bond length | 0.002 |
RMSD bond angle | 0.435 |
Data reduction software | xia2 |
Data scaling software | xia2 |
Phasing software | PHASER |
Refinement software | PHENIX (1.18.1_3865) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 89.000 | 2.690 |
High resolution limit [Å] | 2.640 | 2.640 |
Rmerge | 0.209 | |
Number of reflections | 30147 | 1419 |
<I/σ(I)> | 5 | |
Completeness [%] | 99.2 | 93 |
Redundancy | 9.4 | 5.3 |
CC(1/2) | 0.993 | 0.300 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 25 % (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Tris pH 8.5 |