SAXSdb — 9u37

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1. Structure Basics

entry_id	9u37
deposition_date	2025-03-18
title	D14.F25.S02 IgG complexed to DENV2-US/BID/V594/2006 virus
keywords	Dengue virus, flavivirus, broadly neutralizing antibody, 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	52.04 Å
rg_electron	52.19 Å
i0	1027290000.00
molecular_weight	267090.0 kDa
excluded_volume	334830 Å³
envelope_volume	514500 Å³
shell_volume	84994 Å³
envelope_diameter	203.2 Å
shell_rg	53.40 Å
envelope_rg	51.00 Å
shape_rg	52.18 Å
total_rg	52.26 Å
total_atoms	37214
n_residues	2427
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	189.3 Å
rg_real	52.23 Å
rg_real_error	2.43 Å
i0_real	1.0270e+09
i0_real_error	2.1760e+07
rg_reciprocal	51.88 Å
i0_reciprocal	1027000000.0000
total_estimate	0.8420
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.1 Å
skewness	0.541
kurtosis	0.135
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	67520000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.852

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	D14.F25.S02 Fab light chain
formula_weight	12139.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,D,G
atom_count	37214

QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYKYVSWYQQHPGKAPKLMIYDVTKRPSGVPDRFSGSKSGNTASLTISGLQADDEADYYCCSYAGSYTHVVFGGGTKLTVLVVFGG

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 polymer

description	Envelope Glycoprotein E
formula_weight	54413.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,A

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFICKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKVVLPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKIVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVSLVLVGVVTLYLGVMVQA

Entity 3 polymer

description	D14.F25.S02 Fab heavy chain
formula_weight	14037.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,E,I

QVQLVQSGAEVKKPGSSAKVSCKASGGTFSSYAISWVRQAPGQGLEWMGSIMPIFGTVNYAQKFQGRVTITADESTSTAYMELSRLRSEDTAVYFCARGWGGNYRSADLWIYFDLWGQGTLVTVSSRSG

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 polymer

description	Membrane glycoprotein
formula_weight	8373.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	P,Q,F

SVALVPHVGMGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQRALIFILLTAVAPSMT

Entity 5 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	6

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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	—

resolution	7.65 Å
resolution_method	—
num_particles	1045

fit	/app/data/saxs_computation/u3/9u37/9u37.fit
pddf	/app/data/pr_computation/u3/9u37/9u37.pr.out
profile	/app/data/saxs_computation/u3/9u37/9u37.dat

D14.F25.S02 IgG complexed to DENV2-US/BID/V594/2006 virus

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Entity 5 branched

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)