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9vdt

Crystal structure of voltage-gated sodium channel NavAb N49K DC230 mutant

Method: X-RAY DIFFRACTION D_max: 86.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdt
deposition_date	2025-06-09
title	Crystal structure of voltage-gated sodium channel NavAb N49K DC230 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	26.61 Å
rg_electron	25.19 Å
i0	10087200.00
molecular_weight	31653.0 kDa
excluded_volume	43151 Å³
envelope_volume	57582 Å³
shell_volume	20256 Å³
envelope_diameter	88.4 Å
shell_rg	30.76 Å
envelope_rg	24.34 Å
shape_rg	25.19 Å
total_rg	26.16 Å
total_atoms	2220
n_residues	217
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	86.2 Å
rg_real	26.62 Å
rg_real_error	0.89 Å
i0_real	1.0090e+07
i0_real_error	1.4360e+05
rg_reciprocal	26.62 Å
i0_reciprocal	10090000.0000
total_estimate	0.7740
solution_quality	GOOD a GOOD solution
n_peaks	4
r_peak_primary	38.8 Å
skewness	0.123
kurtosis	-0.678
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	782800.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.746; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.826; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Ion transport protein
formula_weight	31253.1 kDa
mutation	N49K
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2225

GSMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFKQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

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	2

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

Entity 5 non-polymer

description	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	678.9 kDa
src_method	nat
entity_count	8

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	5

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6. Citations (1)

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length_a	129.755 Å
length_b	129.755 Å
length_c	200.315 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	3.500 Å
resolution_low	29.690 Å
r_factor	0.3099
r_work	0.3084
r_free	0.3444

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