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9vel

The composite cryo-EM structure of bacteriophage SPO1 capsid

Method: ELECTRON MICROSCOPY D_max: 250.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vel
deposition_date	2025-06-09
title	The composite cryo-EM structure of bacteriophage SPO1 capsid
keywords	SPO1, Phage, Capsid, 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	94.60 Å
rg_electron	95.66 Å
i0	10241300000.00
molecular_weight	872880.0 kDa
excluded_volume	1095700 Å³
envelope_volume	1910800 Å³
shell_volume	171420 Å³
envelope_diameter	374.0 Å
shell_rg	77.70 Å
envelope_rg	97.93 Å
shape_rg	95.65 Å
total_rg	95.51 Å
total_atoms	61498
n_residues	7883
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	250.6 Å
rg_real	89.58 Å
rg_real_error	0.99 Å
i0_real	9.8020e+09
i0_real_error	2.1180e+08
rg_reciprocal	90.68 Å
i0_reciprocal	10110000000.0000
total_estimate	0.9193
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	94.0 Å
skewness	0.256
kurtosis	-0.749
angular_range	— – 0.0800 Å⁻¹
current_alpha	0.6792
highest_alpha	321800000.0000
n_real_points	17
gnom_version	4.1.3
quality_criteria	AN1: 0.002; Oscil: 0.999; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Gp6.1
formula_weight	51445.0 kDa
src_method	nat
entity_count	16

Polymer

type	polypeptide(L)
strand_id	C,F,G,D,I,J,O,N,M,H,K,L,B,E,P,A
atom_count	61498

MNFGNGVNGFGNGSQADVDALNKALEAGHTVNPLDLEGGGAFRVESLERSLHNLSFTDQHIKFWKKIPKQKAYSTVEQYGQLLDYGRSQGAFVGEGVLPDTNDSTYARKAAFVKFLGTTREVTHPMTLVNSAFGNVIARQNKDGILWMLKQIEQALFWGDSKLAPGGQEGLQFDGINKMIDPENTIDLKGNYLEEKHINWGSQLILQNYGTPTDLMLPFEVMGQFSQEFFPKERVIMPTNDGYQAGVVVNKFMTHGGEVDFTPNLFLNKTTPLNMNASSQKAPAPGTLAAEIGTANDAEFGKQTGGGAGVYKYAVTFNNSHGESVPSNIVDVTIANEDVAKGVKLTITNPVSTAFPVEYIKVYRSEKDGQRLYEVAKFAVTTDNSGGVTEHTDKCEILANTYTAFMGEMSEEVIAFKQLTPMMKMDLATLGPVIRWMILMYGVPVMYAPKKFMKYTNIKADVPGYIGN

Entity 2 polymer

description	Gp29.2
formula_weight	19837.9 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	r,q,s,v

MLFKYIHDVNAKVEEGRRYLSDVVRVALDKEETTDPDTQEVTSTSYRVTAYPVVQVGEEEVPYIPVHPKTAEPGQKVTVPTYDVPEKLPVLVRGRNPEATGDYDDHIWVTEEVEVRPLVDEVFKEDEFEKARLYYENVAAQLAEGDDIRHYYRKDLDREAGHYSVSRYPSF

Entity 3 polymer

description	Gp2.7
formula_weight	6380.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	t

MTKLRLITGTVYTEMSAAEVRSYLQRGSKAGTINGYEDEAKTVPILISVESIEYIYL

Entity 4 polymer

description	Gp36.3
formula_weight	10812.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	w

MNHNIQDLQMHANEVCRQIGAKAVQDYLKKVDPDMVLAYSDERGYFIFDPNEEPPTGSGNGETASQVELYIDLTKPLEGADFRRYESPNPSTITLP

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6. Citations (1)

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resolution	3.00 Å
resolution_method	—
num_particles	626340

fit	/app/data/saxs_computation/ve/9vel/9vel.fit
pddf	/app/data/pr_computation/ve/9vel/9vel.pr.out
profile	/app/data/saxs_computation/ve/9vel/9vel.dat

The composite cryo-EM structure of bacteriophage SPO1 capsid

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)