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9yar

Rana catesbeiana saxiphilin:STX-C13-OBz (co-crystal)

Method: X-RAY DIFFRACTION D_max: 146.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yar
deposition_date	2025-09-16
last_revision	2026-05-27
title	Rana catesbeiana saxiphilin:STX-C13-OBz (co-crystal)
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	44.33 Å
rg_electron	44.00 Å
i0	990347000.00
molecular_weight	168840.0 kDa
excluded_volume	161220 Å³
envelope_volume	328490 Å³
shell_volume	61518 Å³
envelope_diameter	147.7 Å
shell_rg	49.75 Å
envelope_rg	42.91 Å
shape_rg	43.99 Å
total_rg	44.19 Å
total_atoms	12682
n_residues	1636
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	146.4 Å
rg_real	44.31 Å
rg_real_error	1.53 Å
i0_real	9.9030e+08
i0_real_error	1.8880e+07
rg_reciprocal	44.33 Å
i0_reciprocal	990400000.0000
total_estimate	0.8967
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.8 Å
skewness	0.251
kurtosis	-0.570
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	29370000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.884

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Saxiphilin
formula_weight	94228.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	13011

MAPTFQTALFFTIISLSFAAPNAKQVRWCAISDLEQKKCNDLVGSCNVPDITLVCVLRSSTEDCMTAIKDGQADAMFLDSGEVYEASKDPYNLKPIIAEPYSSNRDLQKCLKERQQALAKKMIGHYIPQCDEKGNYQPQQCHGSTGHCWCVNAMGEKISGTNTPPGQTRATCERHELPKCLKERQVALGGDEKVLGRFVPQCDEKGNYEPQQFHGSTGYSWCVNAIGEEIAGTKTPPGKIPATCQKHDLVTTCHYAVAMVKKSSAFQFNQLKGKRSCHSGVSKTDGWKALVTVLVEKKLLSWDGPAKESIQRAMSKFFSVSCIPGATQTNLCKQCKGEEGKNCKNSHDEPYYGNYGAFRCLKEDMGDVAFLRSTALSDEHSEVYELLCPDNTRKPLNKYKECNLGTVPAGTVVTRKISDKTEDINNFLMEAQKRQCKLFSSAHGKDLMFDDSTLQLALLSSEVDAFLYLGVKLFHAMKALTGDAHLPSKNKVRWCTINKLEKMKCDDWSAVSGGAIACTEASCPKGCVKQILKGEADAVKLEVQYMYEALMCGLLPAVEEYHNKDDFGPCKTPGSPYTDFGTLRAVALVKKSNKDINWNNIKGKKSCHTGVGDIAGWVIPVSLIRRQNDNSDIDSFFGESCAPGSDTKSNLCKLCIGDPKNSAANTKCSLSDKEAYYGNQGAFRCLVEKGDVAFVPHTVVFENTDGKNPAVWAKNLKSEDFELLCLDGSRAPVSNYKSCKLSGIPPPAIVTREESISDVVRIVANQQSLYGRKGFEKDMFQLFSSNKGNNLLFNDNTQCLITFDRQPKDIMEDYFGKPYYTTVYGASRSAMSSELISACTIKHCSNSLEVLFQ

Source

organism	Aquarana catesbeiana
common_name	American bullfrog
ncbi_taxonomy_id	8400
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	[(2Z,3aS,4R,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl benzoate
formula_weight	360.4 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	329

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6. Citations (1)

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length_a	95.981 Å
length_b	105.688 Å
length_c	253.280 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	2.400 Å
resolution_low	48.770 Å
r_factor	0.2509
r_work	0.2495
r_free	0.2782

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

Rana catesbeiana saxiphilin:STX-C13-OBz (co-crystal)

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