7Q3Q

Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SOLEIL BEAMLINE PROXIMA 2
Synchrotron site	SOLEIL
Beamline	PROXIMA 2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-10-07
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.980112
Spacegroup name	P 43 21 2
Unit cell lengths	62.451, 62.451, 218.525
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.410 - 2.300
R-factor	0.1866
Rwork	0.185
R-free	0.22020
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6ym0
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHENIX
Refinement software	PHENIX (1.19_4092)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	47.410	47.410	2.380
High resolution limit [Å]	2.300	8.910	2.300
Rmerge	0.115	0.034	1.761
Rmeas	0.116	0.034	1.777
Rpim	0.016	0.005	0.236
Total number of observations	1043029	17413	106171
Number of reflections	20030	436	1923
<I/σ(I)>	32.4	89.4	3.5
Completeness [%]	99.4	99.6	99
Redundancy	52.1	39.9	55.2
CC(1/2)	1.000	1.000	0.886

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	30% PEG 4000, 0.1 M Tris-HCl (pH 8.5) and 0.2 M Li2SO4