SAXSdb — 9vyh

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1. Structure Basics

entry_id	9vyh
deposition_date	2025-07-21
title	Cyanopodophage Pan3 tailspike
keywords	Cyanophage, Virus, Tailspike, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

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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	48.98 Å
rg_electron	48.15 Å
i0	1206400000.00
molecular_weight	282450.0 kDa
excluded_volume	351030 Å³
envelope_volume	473970 Å³
shell_volume	81369 Å³
envelope_diameter	183.1 Å
shell_rg	52.76 Å
envelope_rg	47.70 Å
shape_rg	48.15 Å
total_rg	48.34 Å
total_atoms	19910
n_residues	2695
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	170.3 Å
rg_real	48.73 Å
rg_real_error	1.75 Å
i0_real	1.2060e+09
i0_real_error	2.1730e+07
rg_reciprocal	48.97 Å
i0_reciprocal	1207000000.0000
total_estimate	0.8589
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.2 Å
skewness	0.137
kurtosis	-0.316
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	81210000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Tail spike protein
formula_weight	77739.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	m,n,o
atom_count	19910

MAAQLFYLPFRPMLDANALAVPGAKLYFYATGTTTKQPVYTSSALTTQLPNPVVANAAGKFPAIYLNDALTYRCYIEDADGNELADSDPYLASIADELTDELQDVVDAVEADRVAAANSATAAATSATAAQTAETAAETAQAAAEAVIADPDFVAVSAALTDIGLVADGIADVELVADNIASISSLADTSAPVPQIGLDNQERIETDAAGAILRSITRDGRAVNTIPLGVSGLDTSGQRLAYVTGGDISVIGGSGAAVTVPGVANWTGGPTLSPQLAGIVDGRSVLTINRPFAQAQQAVMVGNDGALAPLPDPDLVHILLADGQSLSIGTNGRWFSTTQMHATPVLPRNIWMLQRSGVSDVRVGRQSDWNAGNSTQVTAEQILGFIPAGPRPLPNVIWSSVIFSESILERAAKIYSDRVFAATGRRPHVLIIAIGVGGISIDNMQKTGAATIPNTTTTKYDQDLVILNRVKALLDAQGKRGVVVGVLRKHGETSSADTAYATKATTQINDLNTDIKSIFGQAGNPIWIEHVQSSHNAAGIESNKALLAMHLAGTLHLAGPDYQLLGRQGFQVTGVTTPPNPDFVHPTARGYAIIAEEMIDQLWQVLAFNRRRLVTRASAAAASGSTIDVTFTSHSGAIEAVASPGWTDPGNLGFTYTDSGGSVPTITGASVLNPTTVRLTMSASVAGRSNRLVRYALNSTAVSGFTATNKPRGMIRDTTSLGTSEVDSETRWAWAVPAEVSVTGA

Entity 2 polymer

description	tailspike gp15
formula_weight	29091.3 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	q,r,p

MPSTLINRRIDFTASGSPLVVSTRDREIAAFTGLTRWYSPADYANGHWPDRLNGVEQGVMLSHSHSSTTPTTATIGGDTYVNQAGNGRLVGFEQALINPSAFTLAFVWHPNGLTQTNNWPVCTAFDQVPIPDTNNRALQVYMFNNAGNIQCRVSASGATGNAATNIFSGWSTFPNSVPVIVLIGYSAAAGWFNRVIRTTGVVQNLTNASPTTAQTINLGRLQFGMLFQTTASSNDQGALGDIMVFDRNLFEAGNSAILTSVINRLTTDYL

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.50 Å
resolution_method	—
num_particles	163205

fit	/app/data/saxs_computation/vy/9vyh/9vyh.fit
pddf	/app/data/pr_computation/vy/9vyh/9vyh.pr.out
profile	/app/data/saxs_computation/vy/9vyh/9vyh.dat

Cyanopodophage Pan3 tailspike

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)