8Z06

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRSF(JN.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	2024-03-15
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.979183
Spacegroup name	C 1 2 1
Unit cell lengths	163.036, 65.460, 49.924
Unit cell angles	90.00, 89.85, 90.00

Refinement procedure

Resolution	81.520 - 2.390
R-factor	0.1885
Rwork	0.186
R-free	0.23160
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7f4w
RMSD bond length	0.008
RMSD bond angle	0.946
Phasing software	PHENIX
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	81.520	2.475
High resolution limit [Å]	2.390	2.390
Number of reflections	20999	20999
<I/σ(I)>	17.832
Completeness [%]	99.9
Redundancy	6.8
CC(1/2)	0.800	0.800

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1 M MES monohydrate pH 6.0, 14% (w/v) Polyethylene glycol 4,000