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9r0b

Structure of A16/G9 (vaccinia virus) in complex with VHH D07 at pH 6.5

Method: X-RAY DIFFRACTION D_max: 139.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r0b
deposition_date	2025-04-24
title	Structure of A16/G9 (vaccinia virus) in complex with VHH D07 at pH 6.5
keywords	poxvirus, viral fusion, vaccinia virus, mpox virus, 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	38.21 Å
rg_electron	39.83 Å
i0	101418000.00
molecular_weight	78328.0 kDa
excluded_volume	96824 Å³
envelope_volume	130120 Å³
shell_volume	31336 Å³
envelope_diameter	146.0 Å
shell_rg	38.39 Å
envelope_rg	40.42 Å
shape_rg	39.86 Å
total_rg	39.62 Å
total_atoms	5493
n_residues	678
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	139.1 Å
rg_real	39.17 Å
rg_real_error	1.58 Å
i0_real	1.0140e+08
i0_real_error	2.0330e+06
rg_reciprocal	38.58 Å
i0_reciprocal	101400000.0000
total_estimate	0.6842
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	27.1 Å
skewness	0.714
kurtosis	-0.189
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	7965000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.399; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.225; Smooth: 0.467

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Virion membrane protein OPG143
formula_weight	40941.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5707

MKLCILLAVVAFVGLSLGRSAAAVTLNRIKIAPGIADIRDKYMELGFNYPEYNRAVKFAEESYTYYYETSPGEIKPKFCLIDGMSIDHCSSFIVPEFAKQYVLIHGEPCSSFKFRPGSLIYYQNEVTPEYIKDLKHATDYIASGQRCHFIKKDYLLGDSDSVAKCCSKTNTKHCPKIFNNNYKTEHCDDFMTGFCRNDPGNPNCLEWLRAKRKPAMSTYSDICSKHMDARYCSEFIRIIRPDYFTFGDTALYVFCNDHKGNRNCWCANYPKSNSGDKYLGPRVCWLHECTDESRDRKWLYYNQDVQRTRCKYVGGSGLVPRGSGGSGGSHHHHHHHHGGSGTGGLNDIFEAQKIEWHE

Source

organism	Vaccinia virus Western Reserve
ncbi_taxonomy_id	696871
host_organism	Drosophila melanogaster

Entity 2 polymer

description	Entry-fusion complex protein OPG094
formula_weight	37432.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MKLCILLAVVAFVGLSLGAGGVSVELPKRDPPPGVPTDEMLLNVDKMHDVIAPAKLLEYVHIGPLAKDKEDKVKKRYPEFRLVNTGPGGLSALLRQSYAGTAPNCCRTFQRTHYWKKDGKISDKYEEGAVLESCWPDVHDTGKCDVDLFDWCQGDTFDRNICHQWIGSAFNRADRTVEGQQSLINLYNKMQTLCSKDASVPICESFLHHLRAHNTEDSKEMIDYILRQQSADFKQKYMRCSYPTRDKLEESLKYAEPRECWDPECSNANVNFLLTRNYNNLGLCNIVRGSGLVPRGSLEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source

organism	Vaccinia virus Western Reserve
ncbi_taxonomy_id	696871
host_organism	Drosophila melanogaster

Entity 3 polymer

description	VHH D07
formula_weight	16965.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J000

MGEVQLQASGGGLVQPGGSLRLSCAASGIVFSNNRMSWYRQAPGKQREVVATITSGGATDYQDSVEGRFTISRDMAKNTVYLQMNSLKPEDTAVYFCNARRDNFATAIYWGQGTQVTVSSLEHHHHHHHHGSGLVPRGSGLNDIFEAQKIEWHE

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	214

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6. Citations (1)

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length_a	46.460 Å
length_b	146.424 Å
length_c	182.234 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.450 Å
resolution_low	39.230 Å
r_factor	0.2232
r_work	0.2218
r_free	0.2493

fit	/app/data/saxs_computation/r0/9r0b/9r0b.fit
pddf	/app/data/pr_computation/r0/9r0b/9r0b.pr.out
profile	/app/data/saxs_computation/r0/9r0b/9r0b.dat

Structure of A16/G9 (vaccinia virus) in complex with VHH D07 at pH 6.5

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)