8ZER
Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL17UM |
Synchrotron site | SSRF |
Beamline | BL17UM |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-07-06 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.97917 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 72.483, 177.458, 209.861 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 45.170 - 3.100 |
R-factor | 0.22477 |
Rwork | 0.222 |
R-free | 0.28272 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7a91 AlphaFold |
RMSD bond length | 0.017 |
RMSD bond angle | 3.014 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0425) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.420 | 3.200 |
High resolution limit [Å] | 3.100 | 3.100 |
Rmerge | 0.176 | 1.348 |
Rmeas | 0.196 | 1.495 |
Rpim | 0.084 | 0.630 |
Total number of observations | 259702 | 23399 |
Number of reflections | 49491 | 4450 |
<I/σ(I)> | 8 | 1.5 |
Completeness [%] | 98.9 | |
Redundancy | 5.2 | 5.3 |
CC(1/2) | 0.993 | 0.450 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 288 | 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350 |