SAXSdb — 9x3k

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1. Structure Basics

entry_id	9x3k
deposition_date	2025-10-09
title	apo state of Mengla Virus Glycoprotein
keywords	Mengla Virus Glycoprotein, VIRAL PROTEIN; 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	30.49 Å
rg_electron	29.02 Å
i0	148688000.00
molecular_weight	97930.0 kDa
excluded_volume	123400 Å³
envelope_volume	159330 Å³
shell_volume	43889 Å³
envelope_diameter	89.4 Å
shell_rg	37.93 Å
envelope_rg	28.93 Å
shape_rg	28.98 Å
total_rg	30.04 Å
total_atoms	6885
n_residues	822
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	89.8 Å
rg_real	30.26 Å
rg_real_error	0.43 Å
i0_real	1.4870e+08
i0_real_error	2.0400e+06
rg_reciprocal	30.36 Å
i0_reciprocal	148700000.0000
total_estimate	0.9100
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	41.5 Å
skewness	0.010
kurtosis	-0.677
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	83920000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.950

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Envelope glycoprotein
formula_weight	73748.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	6885

MALAKKYLMRIFIISHYFLSYNYGFFLPIVKLDIQPENEIIKSPCNGVVKKTEDIHLMSLTLTGQKTASDPMAASKRWAFKEGVLPKTVAFTEGEEAKDCFNISIVDLQGRSLLLEAPSGIKDYPRCKSIHHIQGQNPHAKGNVLHLWGAFFLYDRIASTTMFKDKVFAEGNVAALVINKTVHHQIFKINKIPQNETIGSCNHTYWRSDAGDGFNTTLAVTNLAYVLSANESTKIFKQMQDDLRKRIENMTSSNLTTLSPEAISNSSDANSSATIAYGTSGASISATTRSATSTLTITTDGQMSPPPTPAPPSPSLKPSTDDIKTPTVLSTTSSSTRSKRSVTVAKQSSANPTGKQRGRGRKGPSTGTLTEEQIERVRMLIQKNVGRVNYNNLPLIAGLTALKKKRQVLETFSGEIELEELIGDEKLDSRFRENLKMILETLRNESYSHFELDIPKTAALKSPEETDPRIHMEYLGSGEEPIQSNGQTDTDCDPSLRIWTPNEEKLAAGVSWIPYFGPGAEGLYTMGLMQNQNDVVCRLRRLANQTAKSLDLLLRVTTEERTYSIINRHAIDFLLARWGGTCRVLGPECCIGVEDLTKNITDQIQQMRRDEQDEYEGWGKGGNWFNSQFGNWLNLGILIFLFLGIIIALSCVCRLFMNLTVY

Source

organism	Dianlovirus menglaense
ncbi_taxonomy_id	3052181
host_organism	Homo sapiens

Entity 2 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1073.0 kDa
src_method	man
entity_count	3

Entity 3 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	3

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

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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	3.080 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.08 Å
resolution_method	—
num_particles	19463

fit	/app/data/saxs_computation/x3/9x3k/9x3k.fit
pddf	/app/data/pr_computation/x3/9x3k/9x3k.pr.out
profile	/app/data/saxs_computation/x3/9x3k/9x3k.dat

apo state of Mengla Virus Glycoprotein

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