SAXSdb — 9scw

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1. Structure Basics

entry_id	9scw
deposition_date	2025-08-12
last_revision	2025-10-08
title	Crystal structure of Coxsackie B1 virus-like particle delta-palxa
keywords	coxsackievirus B1, VIRUS-LIKE PARTICLE, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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	— Å
rg_electron	108.60 Å
i0	32926500000.00
molecular_weight	1542000.0 kDa
excluded_volume	1922200 Å³
envelope_volume	2855000 Å³
shell_volume	230920 Å³
envelope_diameter	393.6 Å
shell_rg	83.74 Å
envelope_rg	108.60 Å
shape_rg	108.50 Å
total_rg	108.50 Å
total_atoms	211656
n_residues	14126
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	292.6 Å
rg_real	103.00 Å
rg_real_error	1.22 Å
i0_real	3.1520e+10
i0_real_error	6.3000e+08
rg_reciprocal	102.80 Å
i0_reciprocal	32350000000.0000
total_estimate	0.9071
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	104.5 Å
skewness	0.209
kurtosis	-0.702
angular_range	— – 0.0700 Å⁻¹
current_alpha	1.1290
highest_alpha	600300000.0000
n_real_points	15
gnom_version	4.1.3
quality_criteria	AN1: 0.003; Oscil: 0.998; Stabil: 0.976; Sysdev: 1.000; Positv: 1.000; Valcen: 0.877; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Capsid protein VP1
formula_weight	29729.5 kDa
src_method	man
entity_count	20

Polymer

type	polypeptide(L)
strand_id	1,A,E,Y,g,I,M,Q,U,c,k,o,s,w,0,8,AC,AG,AK,AO
atom_count	211656

GPVEESVERAMVRVADTVSSRPTNSQVVPSDTMQTRHVKNYHSRSESSIENFLCRAACVYYATYTNNSEKGYAEWVINTRQVAQLRRKLELFTYLRFDLELTFVITSAQQPSTATSVDAPVQTHQIMYVPPGGPVPTKVTDYAWQTSTNPSVFWTEGNAPPRMSIPFISIGNAYSCFYDGWTQFSRNGVYGINTLNNMGTLYMRHVNEAGQGPIKSTVRIYFKPKHVKAWVPRPPRLCQYEKQKNVNFTPTGVTTTRVGITTT

Source

organism	Coxsackievirus B1
ncbi_taxonomy_id	12071
host_organism	Trichoplusia ni

Entity 2 polymer

description	Capsid protein VP2
formula_weight	29137.8 kDa
src_method	man
entity_count	20

Polymer

type	polypeptide(L)
strand_id	2,B,F,Z,h,J,N,R,V,d,l,p,t,x,5,9,AD,AH,AL,AP

SPSAEECGFSDRVRSITLGNSTITTQECANVVVGYGVWPEYLKDNEATAEDQPTQPDVATCRFYTLESVQWMKNSAGWWWKLPDALSQMGLFGQNMQYHYLGRTGYTIHVQCNASKFHQGCLLVVCVPEAEMGCSNLNNTPEFAELSGGDTARMFTDTQIGETNSKKVQTAVWNAGMGVGVGNLTIYPHQWINLRTNNSATIVMPYINSVPMDNMFRHNNLTLMIIPFVPLNYSEGSSPYVPITVTIAPMCAEYNGLRLASSQ

Source

organism	Coxsackievirus B1
ncbi_taxonomy_id	12071
host_organism	Trichoplusia ni

Entity 3 polymer

description	Capsid protein VP3
formula_weight	26268.8 kDa
src_method	man
entity_count	20

Polymer

type	polypeptide(L)
strand_id	3,C,G,a,i,K,O,S,W,e,m,q,u,y,6,AA,AE,AI,AM,AQ

GLPVMTTPGSTQFLTSDDFQSPSAMPQFDVTPEMQIPGRVNNLMEIAEVDSVVPVNNTEANVNSLKAYQIPVQSNSDNGKQVFGFPLQPGANGVLNRTLLGEILNYYTHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGVPKNRKDAMLGTHVIWDVGLQSSCVLCVPWISQTHYRYVVEDEYTAAGYITCWYQTNIVVPADVQSSCDILCFVSACNDFSVRMLKDTPFIRQDTFYQ

Source

organism	Coxsackievirus B1
ncbi_taxonomy_id	12071
host_organism	Trichoplusia ni

Entity 4 polymer

description	Capsid protein VP4
formula_weight	7498.3 kDa
src_method	man
entity_count	10

Polymer

type	polypeptide(L)
strand_id	4,D,H,b,j,L,P,T,X,f

MGAQVSTQKTGAHETGLNASGNSIIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMIKSMPALN

Source

organism	Coxsackievirus B1
ncbi_taxonomy_id	12071
host_organism	Trichoplusia ni

Entity 5 non-polymer

description	MYRISTIC ACID
formula_weight	228.4 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	343.999 Å
length_b	343.999 Å
length_c	457.065 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	120

space_group	P 3 1 2
int_tables_number	149
crystal_system	trigonal

resolution	3.200 Å
resolution_low	97.040 Å
r_factor	0.2941
r_work	0.2932
r_free	0.3097

fit	/app/data/saxs_computation/sc/9scw/9scw.fit
pddf	/app/data/pr_computation/sc/9scw/9scw.pr.out
profile	/app/data/saxs_computation/sc/9scw/9scw.dat

Crystal structure of Coxsackie B1 virus-like particle delta-palxa

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)