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9vds

Crystal structure of voltage-gated sodium channel NavAb N49K/L176W mutant

Method: X-RAY DIFFRACTION D_max: 84.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vds
deposition_date	2025-06-09
title	Crystal structure of voltage-gated sodium channel NavAb N49K/L176W mutant
keywords	ion channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	26.49 Å
rg_electron	25.70 Å
i0	8242950.00
molecular_weight	26399.0 kDa
excluded_volume	35028 Å³
envelope_volume	47601 Å³
shell_volume	16218 Å³
envelope_diameter	87.0 Å
shell_rg	31.77 Å
envelope_rg	24.59 Å
shape_rg	25.71 Å
total_rg	26.61 Å
total_atoms	1866
n_residues	218
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	84.4 Å
rg_real	26.55 Å
rg_real_error	0.77 Å
i0_real	8.2430e+06
i0_real_error	1.2200e+05
rg_reciprocal	26.53 Å
i0_reciprocal	8243000.0000
total_estimate	0.8186
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	42.2 Å
skewness	0.146
kurtosis	-0.797
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	890200.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.702; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ion transport protein
formula_weight	31326.2 kDa
mutation	N49K/L176W
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1866

GSMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFKQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTWESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Source

organism	Aliarcobacter butzleri (strain RM4018)
ncbi_taxonomy_id	367737
host_organism	Escherichia coli

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHAPSO
formula_weight	631.9 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	126.880 Å
length_b	126.880 Å
length_c	204.860 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	tetragonal

resolution	3.700 Å
resolution_low	29.910 Å
r_factor	0.3135
r_work	0.3129
r_free	0.3389

fit	/app/data/saxs_computation/vd/9vds/9vds.fit
pddf	/app/data/pr_computation/vd/9vds/9vds.pr.out
profile	/app/data/saxs_computation/vd/9vds/9vds.dat

Crystal structure of voltage-gated sodium channel NavAb N49K/L176W mutant

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction