9LH2

Crystal structure of SARS-CoV-2 spike receptor-binding domain (Delta) in complex with pH-dependent nanobody MNb-11.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL18U1
Synchrotron site	SSRF
Beamline	BL18U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-04-22
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.97853
Spacegroup name	P 41 21 2
Unit cell lengths	82.135, 82.135, 292.615
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.900 - 2.300
Rwork	0.209
R-free	0.23570
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	8cyj
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.900	2.380
High resolution limit [Å]	2.300	2.300
Rmerge	0.138	0.800
Number of reflections	45744	4466
<I/σ(I)>	20	2.5
Completeness [%]	100.0	100
Redundancy	13.2	13

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291.15	0.09M NPS, 0.1M Tris (base), 0.1M BICINE, pH 8.5, 20% v/v PEG 500* MME, 10 % w/v PEG 20000