7JVB

Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 23-ID-B
Synchrotron site	APS
Beamline	23-ID-B
Temperature [K]	80
Detector technology	PIXEL
Collection date	2020-08-07
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1
Spacegroup name	P 41 21 2
Unit cell lengths	70.716, 70.716, 435.037
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	38.959 - 3.287
R-factor	0.2834
Rwork	0.281
R-free	0.32220
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6waq
RMSD bond length	0.005
RMSD bond angle	1.663
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHENIX
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	38.960	3.405
High resolution limit [Å]	3.287	3.287
Rmerge	0.156	0.591
Rpim	0.108	0.445
Number of reflections	17442	1391
<I/σ(I)>	7.8
Completeness [%]	96.3
Redundancy	6.2
CC(1/2)	1.000	0.811

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	100 mM sodium cacodylate pH 6.5, 1 M sodium citrate