8YZR
The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLL(EG.5.1)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRF BEAMLINE BL02U1 |
| Synchrotron site | SSRF |
| Beamline | BL02U1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2024-03-14 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.979183 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 162.672, 65.388, 50.311 |
| Unit cell angles | 90.00, 90.42, 90.00 |
Refinement procedure
| Resolution | 50.310 - 1.800 |
| R-factor | 0.2256 |
| Rwork | 0.224 |
| R-free | 0.26150 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 7f4w |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.039 |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.13_2998) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 60.670 | 1.863 |
| High resolution limit [Å] | 1.760 | 1.799 |
| Rpim | 0.094 | 0.094 |
| Number of reflections | 41724 | 41724 |
| <I/σ(I)> | 5.6 | |
| Completeness [%] | 84.9 | |
| Redundancy | 4.9 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277 | 0.1 M MES monohydrate pH 6.0, 20% (w/v) Polyethylene glycol 2,000 |
