← Back to search

9y91

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

Method: X-RAY DIFFRACTION D_max: 105.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y91
deposition_date	2025-09-12
last_revision	2026-05-27
title	Nanorana parkeri saxiphilin:STX-C13-NBz (co-crystal)
keywords	Saxiphilin, Toxin resistance, Saxitoxin, ANTITOXIN; ANTITOXIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.46 Å
rg_electron	31.89 Å
i0	263099000.00
molecular_weight	85244.0 kDa
excluded_volume	81610 Å³
envelope_volume	145900 Å³
shell_volume	38435 Å³
envelope_diameter	106.9 Å
shell_rg	38.64 Å
envelope_rg	31.32 Å
shape_rg	31.85 Å
total_rg	32.35 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

▼

3. P(r) Analysis (GNOM)

dmax	105.5 Å
rg_real	32.44 Å
rg_real_error	0.78 Å
i0_real	2.6310e+08
i0_real_error	3.8840e+06
rg_reciprocal	32.45 Å
i0_reciprocal	263100000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	38.8 Å
skewness	0.277
kurtosis	-0.521
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	17210000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.925

▶

4. Crystallography & Experiment

▶

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	6848

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	N-{[(2Z,3aS,4S,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl}benzamide
formula_weight	359.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	400

▶

6. Citations (1)

▶

length_a	228.982 Å
length_b	228.982 Å
length_c	67.487 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	1.950 Å
resolution_low	43.270 Å
r_factor	0.1955
r_work	0.1941
r_free	0.2228

fit	/app/data/saxs_computation/y9/9y91/9y91.fit
pddf	/app/data/pr_computation/y9/9y91/9y91.pr.out
profile	/app/data/saxs_computation/y9/9y91/9y91.dat

Nanorana parkeri saxiphilin:STX-C13-NBz (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