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9vdu

Crystal structure of voltage-gated sodium channel NavAb N49K/L176F DC230 mutant

Method: X-RAY DIFFRACTION D_max: 84.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdu
deposition_date	2025-06-09
title	Crystal structure of voltage-gated sodium channel NavAb N49K/L176F 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	26.52 Å
rg_electron	25.06 Å
i0	9755530.00
molecular_weight	30610.0 kDa
excluded_volume	41584 Å³
envelope_volume	55663 Å³
shell_volume	19725 Å³
envelope_diameter	86.7 Å
shell_rg	30.57 Å
envelope_rg	24.11 Å
shape_rg	25.07 Å
total_rg	26.01 Å
total_atoms	2150
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	84.3 Å
rg_real	26.51 Å
rg_real_error	0.77 Å
i0_real	9.7560e+06
i0_real_error	1.4290e+05
rg_reciprocal	26.52 Å
i0_reciprocal	9756000.0000
total_estimate	0.8542
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	40.7 Å
skewness	0.078
kurtosis	-0.720
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	730000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.948

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Ion transport protein
formula_weight	26900.2 kDa
mutation	N49K/L176F
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2155

GSMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFKQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTFESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQ

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	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	678.9 kDa
src_method	syn
entity_count	7

Entity 5 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	128.520 Å
length_b	128.520 Å
length_c	200.790 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	3.400 Å
resolution_low	29.680 Å
r_factor	0.2560
r_work	0.2538
r_free	0.3039

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