9Y7F

Crystal structure of nanobody R3D8 in complex with human voltage-gated sodium channel Nav1.7 P-loop 1.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Synchrotron site	Australian Synchrotron
Beamline	MX2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-03-22
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.95372
Spacegroup name	P 1 21 1
Unit cell lengths	38.829, 43.636, 42.325
Unit cell angles	90.00, 107.84, 90.00

Refinement procedure

Resolution	36.960 - 1.700
R-factor	0.2089
Rwork	0.205
R-free	0.24590
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.056
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	43.640	1.730
High resolution limit [Å]	1.700	1.700
Rmerge	0.100	0.938
Rmeas	0.109	1.028
Rpim	0.042	0.410
Total number of observations	97124	4138
Number of reflections	14888	693
<I/σ(I)>	9.9	1.5
Completeness [%]	99.3
Redundancy	6.5	6
CC(1/2)	0.995	0.580

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	12 %w/v PEG 8000, 50 mM Sodium Cacodylate pH 6.5, 90 mM NH4SO4.