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9yav

Rana catesbeiana saxiphilin mutant - F561A

Method: X-RAY DIFFRACTION D_max: 142.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yav
deposition_date	2025-09-16
last_revision	2026-05-27
title	Rana catesbeiana saxiphilin mutant - F561A
keywords	Saxiphilin, Toxin resistance, Saxitoxin, ANTITOXIN; ANTITOXIN
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	44.77 Å
rg_electron	44.26 Å
i0	520652000.00
molecular_weight	182230.0 kDa
excluded_volume	225820 Å³
envelope_volume	331480 Å³
shell_volume	61900 Å³
envelope_diameter	150.5 Å
shell_rg	49.87 Å
envelope_rg	43.12 Å
shape_rg	44.28 Å
total_rg	44.46 Å
total_atoms	12737
n_residues	1652
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	142.3 Å
rg_real	44.75 Å
rg_real_error	1.08 Å
i0_real	5.2070e+08
i0_real_error	8.0770e+06
rg_reciprocal	44.77 Å
i0_reciprocal	520700000.0000
total_estimate	0.8809
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.8 Å
skewness	0.261
kurtosis	-0.542
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	27340000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.564

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Saxiphilin
formula_weight	94152.2 kDa
mutation	F561A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	13107

MAPTFQTALFFTIISLSFAAPNAKQVRWCAISDLEQKKCNDLVGSCNVPDITLVCVLRSSTEDCMTAIKDGQADAMFLDSGEVYEASKDPYNLKPIIAEPYSSNRDLQKCLKERQQALAKKMIGHYIPQCDEKGNYQPQQCHGSTGHCWCVNAMGEKISGTNTPPGQTRATCERHELPKCLKERQVALGGDEKVLGRFVPQCDEKGNYEPQQFHGSTGYSWCVNAIGEEIAGTKTPPGKIPATCQKHDLVTTCHYAVAMVKKSSAFQFNQLKGKRSCHSGVSKTDGWKALVTVLVEKKLLSWDGPAKESIQRAMSKFFSVSCIPGATQTNLCKQCKGEEGKNCKNSHDEPYYGNYGAFRCLKEDMGDVAFLRSTALSDEHSEVYELLCPDNTRKPLNKYKECNLGTVPAGTVVTRKISDKTEDINNFLMEAQKRQCKLFSSAHGKDLMFDDSTLQLALLSSEVDAFLYLGVKLFHAMKALTGDAHLPSKNKVRWCTINKLEKMKCDDWSAVSGGAIACTEASCPKGCVKQILKGEADAVKLEVQYMYEALMCGLLPAVEEYHNKDDFGPCKTPGSPYTDAGTLRAVALVKKSNKDINWNNIKGKKSCHTGVGDIAGWVIPVSLIRRQNDNSDIDSFFGESCAPGSDTKSNLCKLCIGDPKNSAANTKCSLSDKEAYYGNQGAFRCLVEKGDVAFVPHTVVFENTDGKNPAVWAKNLKSEDFELLCLDGSRAPVSNYKSCKLSGIPPPAIVTREESISDVVRIVANQQSLYGRKGFEKDMFQLFSSNKGNNLLFNDNTQCLITFDRQPKDIMEDYFGKPYYTTVYGASRSAMSSELISACTIKHCSNSLEVLFQ

Source

organism	Aquarana catesbeiana
common_name	American bullfrog
ncbi_taxonomy_id	8400
host_organism	Spodoptera frugiperda

Entity 2 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	370

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6. Citations (1)

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length_a	96.345 Å
length_b	110.241 Å
length_c	254.696 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.230 Å
resolution_low	48.170 Å
r_factor	0.2120
r_work	0.2103
r_free	0.2438

fit	/app/data/saxs_computation/ya/9yav/9yav.fit
pddf	/app/data/pr_computation/ya/9yav/9yav.pr.out
profile	/app/data/saxs_computation/ya/9yav/9yav.dat

Rana catesbeiana saxiphilin mutant - F561A

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)