8ZES
Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed 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) | 0.9792 |
Spacegroup name | I 21 21 21 |
Unit cell lengths | 126.640, 194.240, 264.370 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 74.100 - 3.700 |
R-factor | 0.21056 |
Rwork | 0.207 |
R-free | 0.26888 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7a91 AlphaFold |
RMSD bond length | 0.018 |
RMSD bond angle | 3.344 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0425) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 80.000 | 80.000 | 3.800 |
High resolution limit [Å] | 3.700 | 20.000 | 3.700 |
Rmerge | 0.205 | 0.037 | 2.828 |
Rmeas | 0.228 | 0.043 | 3.162 |
Number of reflections | 34890 | 255 | 2681 |
<I/σ(I)> | 6.6 | ||
Completeness [%] | 99.1 | ||
Redundancy | 5 | ||
CC(1/2) | 0.996 | 0.998 | 0.321 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 288 | 0.15 M DL-Malic acid pH 7.0, 0.1 M Imidazole pH 7.0, 22% PEG MME 550 |