Experiment: 24JS

Crystal structure of voltage-gated sodium channel NavAb N49K mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5YUC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4

Crystal Properties
Matthews coefficient	Solvent content
6.6	81.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.85	α = 90
b = 126.85	β = 90
c = 203.43	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2026-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NanoTerasu BEAMLINE BL09U MX-ES	1	NanoTerasu	BL09U MX-ES

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.5	44.91	96.66	0.07082	0.983	21.15	90.9		10990			68.82

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.5	3.625			0.957	3.11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.5	28.36	1.36	10050	524	92.94	0.2532	0.2521	0.2541	0.2736	0.2752	79.87

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.3515
f_angle_d	0.7026
f_chiral_restr	0.0445
f_plane_restr	0.0054
f_bond_d	0.0028

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1797
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	159

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
DIALS	data scaling
PHENIX	phasing