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9y92

Nanorana parkeri saxiphilin:STX-C13-OBz (co-crystal)

Method: X-RAY DIFFRACTION D_max: 105.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y92
deposition_date	2025-09-12
last_revision	2026-05-27
title	Nanorana parkeri 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	32.43 Å
rg_electron	31.86 Å
i0	263059000.00
molecular_weight	85246.0 kDa
excluded_volume	81617 Å³
envelope_volume	145630 Å³
shell_volume	38411 Å³
envelope_diameter	107.2 Å
shell_rg	38.58 Å
envelope_rg	31.31 Å
shape_rg	31.82 Å
total_rg	32.32 Å
total_atoms	6427
n_residues	821
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	105.4 Å
rg_real	32.41 Å
rg_real_error	0.69 Å
i0_real	2.6310e+08
i0_real_error	4.0580e+06
rg_reciprocal	32.42 Å
i0_reciprocal	263100000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	38.7 Å
skewness	0.278
kurtosis	-0.518
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	17310000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.926

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Saxiphilin
formula_weight	94703.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6841

MALTFHTALYFTIVGLSFAASDARHVQWCTISHLEQKKCNDLVGSCNVPDITLACVYRSSTENCMAAIKDGQADAMFLDSGDVYKASLDHYNLKPIIAEPYSLHRELTKCLKHRQESLGGDKMVKGRYIPQCDEKGNYHPVQCHASTGYCWCVNANGEKIEGTNTTPVQTPPTCPSQVLTKCLKERQEALGGKRIAIGRYIPQCDEQGNYRPMQCHGSTGYCWCVNAIGEKIEGTNTPPGNTQPTCQSHDWDTCHYAVAVVKNSSTFQFGQLKGKRSCHSGLSKTDGWNAPVNVFVEKKLLPWDGLAKGSIERAVSKFFSASCIPGATETNLCKQCIGEEEKKCKSSHDEPYYGDHGAFRCLQEDKGDVAFLKNTALPDEHSGVYELLCPDNTRKPLNKYKECNLGKVPADAVVTRKAGDKTKDINDFLLEAQKKKCKLFGSPHGKDLMFDDSTTHLAPLPSEIDAFFFLGVKWYNAMKALTEDVKLPSKNKVRWCTINKPEMMKCKDWAAVSGGAIACTEASCPEHCVKQILKGEADAVTLDVQYMYMALMCGLLPAVEEYPNKDDFHPCQIPGSTIKDFGTKRAVALVKKSNKDIKWNNLKGKKSCHTHVGDIPGWVIPAGLISNQNDNIDIESFFGESCAPGSDTNSKLCKLCIGDPENPKASTRCSLSDKEAYYGNEGAFRCLVEKGDVAFVPHTVVFANTDGKNPAEWAKDLKSEDFEILCLDGSRAPVTNYRGCNLSGLPPRAIVTREESVSDVVRILINQQSLYGRNGFEKDMFQMFSSAKGQNLLFNDETQCLIEFDRQPKDIMEDYFGVRYYTAVYSASRSAVPSELIPACTFKHCSNSLEVLFQ

Source

organism	Nanorana parkeri
ncbi_taxonomy_id	125878
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 3 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	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	400

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6. Citations (1)

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length_a	228.643 Å
length_b	228.643 Å
length_c	67.180 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	9

space_group	H 3
int_tables_number	146
crystal_system	—

resolution	1.900 Å
resolution_low	43.210 Å
r_factor	0.1990
r_work	0.1977
r_free	0.2256

fit	/app/data/saxs_computation/y9/9y92/9y92.fit
pddf	/app/data/pr_computation/y9/9y92/9y92.pr.out
profile	/app/data/saxs_computation/y9/9y92/9y92.dat

Nanorana parkeri 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