8R80
SARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab 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 | 2023-11-13 |
Detector | DECTRIS EIGER2 XE 16M |
Wavelength(s) | 0.97629 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 108.538, 126.398, 164.824 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 65.640 - 4.030 |
R-factor | 0.2706 |
Rwork | 0.268 |
R-free | 0.31330 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.002 |
RMSD bond angle | 0.466 |
Data reduction software | xia2 |
Data scaling software | xia2 |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 66.000 | 4.090 |
High resolution limit [Å] | 4.030 | 4.030 |
Rmerge | 0.386 | |
Rpim | 0.109 | |
Number of reflections | 19426 | 923 |
<I/σ(I)> | 5.4 | 0.4 |
Completeness [%] | 100.0 | 99.1 |
Redundancy | 13.4 | |
CC(1/2) | 0.995 | 0.250 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Calcium acetate hydrate, 0.1 M sodium cacodylate pH 6.5, 40% PEG 300. |