9RN6

Crystal structure of a protein mimic of SARS-CoV-2 spike's HR1 domain in complex with two nanobodies bound to different epitopes

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ALBA BEAMLINE XALOC
Synchrotron site	ALBA
Beamline	XALOC
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-05-16
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97934
Spacegroup name	P 2 21 21
Unit cell lengths	47.560, 67.340, 230.780
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	19.990 - 2.400
R-factor	0.2474
Rwork	0.247
R-free	0.26310
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.737
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	19.990	2.490
High resolution limit [Å]	2.400	2.400
Rmerge	0.078	1.121
Rmeas	0.085	1.210
Rpim	0.032	0.449
Total number of observations	212001	22131
Number of reflections	29937	3097
<I/σ(I)>	12.4	1.9
Completeness [%]	99.8
Redundancy	7.1	7.1
CC(1/2)	0.999	0.807

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	288	0.15 M NaCl, PEG 6000 50% (v/v), 0.1 M Tris/HCl