8YDV

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL45XU
Synchrotron site	SPring-8
Beamline	BL45XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-10-18
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1
Spacegroup name	P 41
Unit cell lengths	87.480, 87.480, 118.230
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.980 - 2.200
R-factor	0.1966
Rwork	0.195
R-free	0.22100
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.510
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.330
High resolution limit [Å]	2.200	2.200
Number of reflections	45117	7081
<I/σ(I)>	11.99
Completeness [%]	100.0
Redundancy	10.5
CC(1/2)	0.998	0.564

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES (pH 7.5), 10% PEG 6000, 5% MPD