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9udo

Single-chain Fv antibody of F8 complex with NNP-Cap

Method: X-RAY DIFFRACTION D_max: 57.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9udo
deposition_date	2025-04-07
title	Single-chain Fv antibody of F8 complex with NNP-Cap
keywords	ANTIGEN BINDING, AFFINITY MATURATION, SOMATIC HYPERMUTATION, IMMUNE SYSTEM; IMMUNE SYSTEM
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	18.37 Å
rg_electron	17.41 Å
i0	22465600.00
molecular_weight	23885.0 kDa
excluded_volume	22948 Å³
envelope_volume	36487 Å³
shell_volume	17570 Å³
envelope_diameter	60.1 Å
shell_rg	23.49 Å
envelope_rg	17.69 Å
shape_rg	17.38 Å
total_rg	18.15 Å
total_atoms	1807
n_residues	236
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	57.3 Å
rg_real	18.28 Å
rg_real_error	0.20 Å
i0_real	2.2470e+07
i0_real_error	2.5060e+05
rg_reciprocal	18.30 Å
i0_reciprocal	22470000.0000
total_estimate	0.9035
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	56.5 Å
skewness	0.214
kurtosis	-0.425
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	7201000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Single-chain Fv antibody of F8
formula_weight	25880.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1992

GSQAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNRWVFGGGTKLTVLGGGGGSGGGGSGGGGSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYRVYYAMDYWGQGTSVTVSS

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 non-polymer

description	6-[2-(4-hydroxy-3,5-dinitrophenyl)acetamido]hexanoic acid
formula_weight	355.3 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	152

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6. Citations (1)

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length_a	136.770 Å
length_b	34.950 Å
length_c	46.210 Å
angle_alpha	90.00 °
angle_beta	99.26 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.880 Å
resolution_low	40.970 Å
r_factor	0.2222
r_work	0.2207
r_free	0.2508

fit	/app/data/saxs_computation/ud/9udo/9udo.fit
pddf	/app/data/pr_computation/ud/9udo/9udo.pr.out
profile	/app/data/saxs_computation/ud/9udo/9udo.dat

Single-chain Fv antibody of F8 complex with NNP-Cap

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