SAXSdb — 9rch

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1. Structure Basics

entry_id	9rch
deposition_date	2025-05-29
title	Cryo-EM structure of Yadonushi Virus 1
keywords	CryoEM, Virion, Yadokari, Mycovirus, 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	44.65 Å
rg_electron	44.59 Å
i0	745617000.00
molecular_weight	226600.0 kDa
excluded_volume	284140 Å³
envelope_volume	379970 Å³
shell_volume	71097 Å³
envelope_diameter	170.0 Å
shell_rg	48.74 Å
envelope_rg	45.09 Å
shape_rg	44.57 Å
total_rg	44.83 Å
total_atoms	15969
n_residues	1995
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	158.7 Å
rg_real	44.81 Å
rg_real_error	1.83 Å
i0_real	7.4560e+08
i0_real_error	1.4410e+07
rg_reciprocal	44.66 Å
i0_reciprocal	745500000.0000
total_estimate	0.8536
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.9 Å
skewness	0.461
kurtosis	-0.118
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	172000000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.877

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Coat protein
formula_weight	111298.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	15969

TTFSNFMTNVLGKTSSSKGVISLKQISSSISHLIPDTPRADTNNNRASYFYRVRRLLTRAMRNQSVPYVPVYEHNPVASYKIVRYDTFEVSNKLVLKKAKTVDVSARSISLTQDISLSTLKAEIIDSTNNIKTFNNNWITMMDVQKPIADVFKVLSLRSENNRVFWDTGLYNYFSNFADVTSSSFFPIALNKTLRHHAMTSSMSIGAFNQLEARTPDLKFDPLVAEPKIQDKLYPLFNHDISDINAYTVPLPVFIFMMFPQHFRKEIIVDYMLAFSFGNRTINERENFLLQAIRPRLQEILTLNAEPVQLPTNAHDFAIKLDNIGVFIEGLTTSAPAVRSFFDSLHKLSTGYADFRIRGTPLRAINLPFTVILSEDFDQTTRATVPLNENDFLKKHDAIEKMVSMLPHPIFQYAIEVEQTINLPGNGQNTLAKNTSKDLFMPVASLVNQFHKKNQLLCVDIVPHQGGSIRSNFTYNDGTVASEYRYPITLLSKDGTKAKVDIIDQMTKPVSVLKDIKEHLTYSRDNVNRLNASMNQSMSCMLTETELADLLNLTANLTHVTPLPTTVHDISQTEDKLDIHYINTPRIGLTGYKIKADDMTDDEYIISDTYVANVTDGITNVAFNRFRDHTPSSDLGGANKFIAHPDYVIPFFDHDWFVFITAGLLNFQWPDIIGKVTTNTVFEHNATLDAIATEQIRLIDTYTDTKNIPMRDTFFPPGNDVRDSLEVISITNSIAMDDSVLNQVAHAFSTQSYTCSHPYKLDYDGNEYLDNLLACSTNHVPIRFTQMNMVNPLPILSNLEKDFERATINNTPNKEGVVRSQRRRRPEDNFLRMITQIITRFDFSGFSTVNENNMVTLRDAATNQKISAYQRYTTNLSQIKYFISLCIRLGTLQTFNDITGTSTTRVKTPTYPTHLLAVNVITQTEYRISLNKEEYWSHLKSSIVITTPTDVSVEQEQIFDDININRNVNRVKPSFSNL

Entity 2 polymer

description	Coat protein
formula_weight	115597.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IKKMFDTQTNLYNAIRNTAMTMNIPLTSQLDTATLPPASTTFSNFMTNVLGKTSSSKGVISLKQISSSISHLIPDTPRADTNNNRASYFYRVRRLLTRAMRNQSVPYVPVYEHNPVASYKIVRYDTFEVSNKLVLKKAKTVDVSARSISLTQDISLSTLKAEIIDSTNNIKTFNNNWITMMDVQKPIADVFKVLSLRSENNRVFWDTGLYNYFSNFADVTSSSFFPIALNKTLRHHAMTSSMSIGAFNQLEDRTPDLKFDPLVAEPKIQDKLYPLFNHDISDINAYTVPLPVFIFMMFPQHFRKEIIVDYMLAFSFGNRTINERENFLLQAIRPRLQEILTLNAEPVQLPTNAHDFAIKLDNIGAFIEGLTTSAPAVRSFFDSLHKLSTGYADFRIRGTPLRAINLPFTVILSEDFDQTTRATVPLNENDFLKKHDAIEKMVSMLPHPIFQYAIEVEQTINLPGNGQNTLAKNTSKDLFMPVASLVNQFHKKNQLLCVDIVPHQGGSIRSNFTYNDGTVASEYRYPITLLSKDGTKAKVDIIDQMTKPVSVLKDIKEHLTYSRDNVNRLNASMNQSMSCMLTETELADLLNLTANLTHVTPLPTTVHDISQTEDKLDIHYINTPRIGLTGYKIKADDMTDDEYIISDTYVANVTDGITNVAFNRFRDHTPSSDLGGANKFIAHPDYVIPFFDHDWFVFITAGLLNFQWPDIIGKATTNTVFEHNATLDAIATQQIRLIDTYTDTKNIPMRDTFFPPGNDVRDSLEVISITNSIAMDDSVLNQVAHAFSTQSYTCSHPYKLDYDGNEYLDNLLACSTNHVPIRFTQMNMVNPLPILSNLEKDFERATINNTPNKEGVVRSQRRRRPEDNFLRMITQIITRFDFSGFSTVNENNMVTLRDAATNQKISAYQRYTTNLSQIKYFISLCIRLGTLQTFNDITGTSTTRVKTPTYPTHLLAVNVITQTEYRISLNKEEYWSHLKSSIVITTPTDVSVEQEQIFDDININRNVNRVKPSFSNL

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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	2.20 Å
resolution_method	—
num_particles	550000

fit	/app/data/saxs_computation/rc/9rch/9rch.fit
pddf	/app/data/pr_computation/rc/9rch/9rch.pr.out
profile	/app/data/saxs_computation/rc/9rch/9rch.dat

Cryo-EM structure of Yadonushi Virus 1

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

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)