8CWV

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 23-ID-D
Synchrotron site	APS
Beamline	23-ID-D
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-10-31
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1.03320
Spacegroup name	C 2 2 21
Unit cell lengths	89.310, 142.024, 149.367
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	42.780 - 2.510
R-factor	0.239
Rwork	0.238
R-free	0.26400
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7JMW; 7KN5
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX (1.19.2_4158)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.540
High resolution limit [Å]	2.500	6.780	2.500
Rmerge	0.147	0.088	1.120
Rmeas	0.173	0.102	1.332
Rpim	0.088	0.050	0.700
Total number of observations	90065
Number of reflections	27562	1513	1344
<I/σ(I)>	4.3
Completeness [%]	84.0	85.5	81.9
Redundancy	3.3	3.7	3.1
CC(1/2)		0.978	0.459

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	293	40% MPD, 0.1M cacodylate pH 6.5 5% (w/v) PEG-8000, final pH 7.0