8H5U

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-021

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL19U1
Synchrotron site	SSRF
Beamline	BL19U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-07-10
Detector	DECTRIS PILATUS3 S 6M
Wavelength(s)	0.97852
Spacegroup name	P 21 21 21
Unit cell lengths	78.072, 104.827, 107.053
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	40.686 - 2.401
R-factor	0.2262
Rwork	0.225
R-free	0.24510
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yz5 6b20
RMSD bond length	0.004
RMSD bond angle	0.725
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX (1.10.1_2155)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.490
High resolution limit [Å]	2.400	2.400
Rmerge	0.173	0.722
Number of reflections	33895	3240
<I/σ(I)>	25.692
Completeness [%]	97.9
Redundancy	11.9

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M sodium citrate tribasic dihydrate, pH 5.0, 18% w/v polyethylene glycol 20000