SAXSdb — 9vs4

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1. Structure Basics

entry_id	9vs4
deposition_date	2025-07-08
title	Structure of Ebinur lake virus polymerase complexed with suramin
keywords	Viral protein, polymerase, suramin; 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	34.98 Å
rg_electron	34.06 Å
i0	363336000.00
molecular_weight	158440.0 kDa
excluded_volume	200270 Å³
envelope_volume	253330 Å³
shell_volume	59567 Å³
envelope_diameter	111.0 Å
shell_rg	42.50 Å
envelope_rg	33.53 Å
shape_rg	34.05 Å
total_rg	34.71 Å
total_atoms	11134
n_residues	1360
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	107.5 Å
rg_real	34.75 Å
rg_real_error	0.49 Å
i0_real	3.6330e+08
i0_real_error	5.3760e+06
rg_reciprocal	34.89 Å
i0_reciprocal	363400000.0000
total_estimate	0.6828
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	45.4 Å
skewness	0.073
kurtosis	-0.534
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0002
highest_alpha	59390000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.973; Smooth: 0.934

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	199038.4 kDa
ec_number	2.7.7.48
mutation	D79A,D92A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11134

MEDPMYEQFLQRIQAVRTATVAKDISADILEARHDYFGRELCRALDIEYRNNVLLDEIILDVYPGVNLMEYNVPHVTPANYIWTGDMLLILAYKVSVGHDSTEVTYKKYTTLILPVMQEIGINTEICIIRANPVTNQISIVGEQFKRLFPTIPVELNFARFFELRKMLLDKFADDEEFLMMIAHGDFTLTAPWCQDDTPELIDHPIYQEFLGSMPPRFVSMFEEAMDFSAYNAERWNTLLYKIKNLTLEDYQDYLNIKSHNIFNMTGDFMKPTQDEIDIGWESMSKRISQERELTTDINKQKPSIHFIWAQNKDRKLLNSTAKLVFLSNTLQSITEQSTWTDALKAIGVSMDIGNNIGLYENLCAERKLIARSTGKKVNNKRLEAVKIGKALVLWEQQFILANELFKGQERQKFIKNFFGIGKHKTFKDKTSEDLDREKPKILDFNNTRVLMAARTMVNKNKKFLSQDNTLEFDHPIISTYFDQVREASIDTAQVLKKISKTCFWQAITDISTLMRNILAVSQYNRHNTFRVAMCANDSIYGLVFPSSDIKTKRATIVFCIVCMHNSRDDIMDAGALFTTLETKTKTFVSISKAIRLDKERCQRIVSSPGLFILSTLLLYNNNTEISLYDVMNFTFYTSLSITKSMLSLTEPSRYMIMNSLAISSHVRDYIAEKFSPYTKTLFSVYMVNLIKRGCATANEQSEKIQVRNIYLSDYDITQKGINDIRNLDSIWFPGKVNLKEYINQIYLPFYFNAKGLHEKHHVMIDLAKTVLEIEMNQRLDQLGIWSKNEKKQHVNLPILVHSIAKSLILDTSRHNHLRNRVESRNNFRRSISTISTFTSSKSCIKIGEFQDLKTKEFKATKKMNEKINQKFRLANPLFIDDKDADAEIMHCNYDQLKTKVPNYKDYISVKVFDRLYELYKTKELDDKPFIEQAMKMMKEHKEFNFTFFNKGQKTSKDREIFVGEFEAKMCMYVVERISKERCKLNEDEMISEPGDTKLRILEKKAEEEIRYIVEKTKDSILKGDPAHALKLEINADMSKWSAQDVFFKYFWLVAMDPILYPSEKKRILYFMCNYMQKNLILPDDLLSNIMDQRRPYENDIILESTNGLAQNFVQIKRNWLQGNFNYMSSYVHSCAMLVYKDVAKEAVKLLDGNCLVNSMVHSDDNQTSLSIIQNKLKDNMIIEYVAKLFEAVCLAFGCQANMKKTYITHTCKEFVSLFNLHGEPLSIYGRFLLPSVGDCAYIGPYEDLASRLSAAQQSLKHGCPPSYVWVAISCSHWITHFTYNMMHDQVNSPMQYLPFEDRFQVPTELNGYLSAPLYLIALIGIEADNLWFLLNILKKLVPLDKQKETIQTQFTAIQDNINKLTPSELFRLKLLRYLTLDTEITSDSNMGETSDMRSRSLLTPRKFTTAGSLNKLVSYNDFKNAMNTNEFQENLEYMEMNPELLVTKGENKEQYINSILFRYNSKRFKESLSIQAPSQLFVEQILFSHKPIIDYSSIFDKLASMAETEIIENLPDIIGRVTYPQAYQMITRDITQLPLDIDDIKIVFKYCVLNDPLIITAANTSLLCVRGAPQDRTGLSACQMPEFRNMKLIHHSPALVLKAFSKGTVDIPGADPVELEKDLLHLKEFVENTGIQEKIQMNIDNPPKHLQGTEVLIYKIRELTKLYQVCYDYVKSTEHKVKVFILPMKSYTSIEFCTLIQGNTISDSKWYTMH

Source

organism	Ebinur lake virus
ncbi_taxonomy_id	1501396
host_organism	Pichia

Entity 2 non-polymer

description	;8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID ;
formula_weight	1297.3 kDa
src_method	syn
entity_count	2

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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	3.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.00 Å
resolution_method	—
num_particles	85378

fit	/app/data/saxs_computation/vs/9vs4/9vs4.fit
pddf	/app/data/pr_computation/vs/9vs4/9vs4.pr.out
profile	/app/data/saxs_computation/vs/9vs4/9vs4.dat

Structure of Ebinur lake virus polymerase complexed with suramin

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)