8CWU

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 1-21

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 1 2 1
Unit cell lengths	119.151, 55.465, 59.561
Unit cell angles	90.00, 105.90, 90.00

Refinement procedure

Resolution	47.540 - 1.710
R-factor	0.186
Rwork	0.185
R-free	0.20320
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	1.740
High resolution limit [Å]	1.710	4.640	1.710
Rmerge	0.103	0.041	0.659
Rmeas	0.119	0.046	0.776
Rpim	0.058	0.021	0.398
Total number of observations	154126
Number of reflections	39711	2053	1851
<I/σ(I)>	5.2
Completeness [%]	98.1	97.5	92.4
Redundancy	3.9	4.3	3.2
CC(1/2)		0.997	0.513

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	10.5	293	20% polyethylene glycol 8000, 0.1 M NaCl, 0.1 M CAPS pH 10.5