SAXSdb — 9qt3

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1. Structure Basics

entry_id	9qt3
deposition_date	2025-04-07
last_revision	2025-11-19
title	Structure of vaccinia virus A26 (residues 1-397) in complex with Fab 8M2110
keywords	vaccinia virus mpox virus orthopoxvirus neutralizing antibody, VIRAL PROTEIN; VIRAL PROTEIN
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	51.79 Å
rg_electron	51.38 Å
i0	2315960000.00
molecular_weight	401000.0 kDa
excluded_volume	500660 Å³
envelope_volume	707460 Å³
shell_volume	112120 Å³
envelope_diameter	183.6 Å
shell_rg	57.16 Å
envelope_rg	50.28 Å
shape_rg	51.35 Å
total_rg	51.66 Å
total_atoms	28269
n_residues	3563
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	172.0 Å
rg_real	51.70 Å
rg_real_error	1.26 Å
i0_real	2.3160e+09
i0_real_error	4.2200e+07
rg_reciprocal	51.86 Å
i0_reciprocal	2316000000.0000
total_estimate	0.8607
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	63.1 Å
skewness	0.320
kurtosis	-0.201
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0001
highest_alpha	210200000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.785

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Envelop protein OPG153
formula_weight	52359.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,E,I,M
atom_count	28702

MANIINLWNGIVPTVQDVNVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENKKSPLGAPMQWLTQYYILKNEYHKTMLAYDNGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNFINERIKYACKQILHGQLTIALRIRNKFMFIGSPMYLWFNVNGSQVYHDIYDRNAGFHNKEIGRLLYAFMYYLSISGRFLNDFALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYVEFNKKGIAKVTEDKPDNDKRIHAIRLINDSTDVQHIHFGFRNMVIIDNECANIQSSAENATDTGHHQDSKINIEVEDDVIDDDDYNPKPTPIPEPHPRPPFPRHEGSGLVPRIGSGSAGWSHPQFEKGGGSGGGSGGGSWSHPQFEKGTGGLNDIFEAQKIEWHE

Source

organism	Vaccinia virus Western Reserve
ncbi_taxonomy_id	696871
host_organism	Escherichia coli

Entity 2 polymer

description	Heavy chain of Fab 8M2110
formula_weight	23980.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,F,J,N

QVQLQESGPGLVKPSETLSLTCSVSGGSISTYYWSWIRQPAGKGLEWIGLMYNSGSPNYNPSLKSRVTMSGDTSKNQFSLKLSSVTAADTAVYYCARLRYDFWSGSKGRYYMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Light chain of Fab 8M2110
formula_weight	23449.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,G,K,O

DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGQAPKLLIHDASNLETGVPSRFSGSGSGTDFTFTVSSLQAEDIATYYCQQYYNLPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Anti-Fab VHH
formula_weight	13390.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,H,L,P

GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	433

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6. Citations (1)

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length_a	119.405 Å
length_b	119.405 Å
length_c	632.812 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	2.900 Å
resolution_low	39.080 Å
r_factor	0.2023
r_work	0.2005
r_free	0.2357

fit	/app/data/saxs_computation/qt/9qt3/9qt3.fit
pddf	/app/data/pr_computation/qt/9qt3/9qt3.pr.out
profile	/app/data/saxs_computation/qt/9qt3/9qt3.dat

Structure of vaccinia virus A26 (residues 1-397) in complex with Fab 8M2110

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)