7PR0

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-07-01
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.97625
Spacegroup name	C 1 2 1
Unit cell lengths	231.308, 146.064, 78.578
Unit cell angles	90.00, 103.68, 90.00

Refinement procedure

Resolution	71.500 - 2.920
R-factor	0.2154
Rwork	0.214
R-free	0.25060
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7pqz
RMSD bond length	0.003
RMSD bond angle	0.635
Data reduction software	xia2
Data scaling software	xia2
Phasing software	PHASER
Refinement software	PHENIX (1.19_4092)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	73.000	2.970
High resolution limit [Å]	2.920	2.920
Rmerge	0.284
Rpim	0.072
Number of reflections	54960	2589
<I/σ(I)>	5.7	0.2
Completeness [%]	99.8	95.6
Redundancy	16.6
CC(1/2)	0.988	0.341

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	10% (w/v) PEG 20 000, 20% (v/v) PEG MME 550, 0.03 M of each NPS (NaNO3; Na2HPO4; (NH4)2SO4) and 0.1 M bicine/Trizma base pH 8.5.