8ZV9

Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF

Replaces:  8IF1

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL19U1
Synchrotron site	SSRF
Beamline	BL19U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-01-10
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97852
Spacegroup name	P 21 21 21
Unit cell lengths	47.060, 167.490, 168.580
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	45.330 - 2.600
R-factor	0.2464
Rwork	0.244
R-free	0.28950
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5hgd
RMSD bond angle	19.056
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX ((1.21_5207: ???))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	45.330	11.620	2.670
High resolution limit [Å]	2.600	8.220	2.600
Rmerge	0.107	0.036	1.181
Rmeas	0.111	0.038	1.230
Number of reflections	42070	931	3020
<I/σ(I)>	18.43
Completeness [%]	99.9
Redundancy	14.4
CC(1/2)	0.999	0.999	0.845

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	287	20% PEG8000, 0.1 M HEPES 7.5