SAXSdb — 9qy3

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1. Structure Basics

entry_id	9qy3
deposition_date	2025-04-16
title	Structure of the Plum Pox Virus (PPV)
keywords	Potyvirus, Plum Pox Virus, PPV, VIRUS; VIRUS
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	71.20 Å
rg_electron	71.61 Å
i0	20310400000.00
molecular_weight	1114800.0 kDa
excluded_volume	1353400 Å³
envelope_volume	2011400 Å³
shell_volume	224180 Å³
envelope_diameter	277.8 Å
shell_rg	78.14 Å
envelope_rg	71.82 Å
shape_rg	71.64 Å
total_rg	71.59 Å
total_atoms	77940
n_residues	9315
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	213.6 Å
rg_real	69.87 Å
rg_real_error	0.71 Å
i0_real	1.9970e+10
i0_real_error	3.4150e+08
rg_reciprocal	70.75 Å
i0_reciprocal	20290000000.0000
total_estimate	0.8401
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	77.7 Å
skewness	0.441
kurtosis	-0.158
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.3584
highest_alpha	2769000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.154

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Coat Protein (CP)
formula_weight	36552.0 kDa
src_method	man
entity_count	45

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s
atom_count	77940

ADEREDDEEVDAGGPTVVTAPAATVATTQPAPVIQPAPQTTAPMFNPIFTPATTQPAVRPVPPISGTKPRSFGVYGNEDASPSTSNTLVNTGRDRDVDAGSIGTFTVPRLKTMTSKLSLPKVKGKAIMNLNHLAHYSPAQVDLSNTRAPQSCFQTWYEGVKRDYDVTDEEMSIILNGLMVWCIENGTSPNINGMWVMMDGETQVEYPIKPLLDHAKPTFRQIMAHFSNVAEAYIEKRNYEKAYMPRYGIQRNLTDYSLARYAFDFYEMTSTTPVRAREAHIQMKAAALRNVQNRLFGLDGNVGTQEEDTERHTAGDVNRNMHNLLGVRGV

Source

organism	Plum pox virus
ncbi_taxonomy_id	12211
host_organism	Plum pox virus

Entity 2 polymer

description	RNA
formula_weight	191003.6 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	t

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

Source

organism	Plum pox virus
ncbi_taxonomy_id	12211
host_organism	Plum pox virus

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	406769

fit	/app/data/saxs_computation/qy/9qy3/9qy3.fit
pddf	/app/data/pr_computation/qy/9qy3/9qy3.pr.out
profile	/app/data/saxs_computation/qy/9qy3/9qy3.dat

Structure of the Plum Pox Virus (PPV)

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

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)