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9uds

Single-chain Fv antibody of C6

Method: X-RAY DIFFRACTION D_max: 111.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uds
deposition_date	2025-04-07
title	Single-chain Fv antibody of C6
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	34.32 Å
rg_electron	33.90 Å
i0	156268000.00
molecular_weight	99628.0 kDa
excluded_volume	124380 Å³
envelope_volume	160950 Å³
shell_volume	41273 Å³
envelope_diameter	113.5 Å
shell_rg	38.92 Å
envelope_rg	33.49 Å
shape_rg	33.88 Å
total_rg	34.33 Å
total_atoms	7030
n_residues	912
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	111.8 Å
rg_real	34.31 Å
rg_real_error	0.89 Å
i0_real	1.5630e+08
i0_real_error	2.4240e+06
rg_reciprocal	34.32 Å
i0_reciprocal	156300000.0000
total_estimate	0.9024
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	38.9 Å
skewness	0.242
kurtosis	-0.627
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	24020000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Single-chain Fv antibody of C6
formula_weight	26116.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7688

GSAQAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYVNWVQEKPDHLFTGLVYSTNSRVPGVPARFSGSLIGDKAALTITGAQAEDEAIYFCTLWYSNHWVFGGGTKLTVLGQGGGGSGGGGSGGGGSQVQLQQPGAELVKPGASVKLSCKTSGYTFPYYWMHWVNQRPGRGLEWIGRIDPNGGGTRYSEKFKSKATLTVDKPSNTAYMQLSSLTSEDSAVYYCARGKLGQHFDYWGQGTALTVSS

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	638

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6. Citations (1)

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length_a	121.236 Å
length_b	116.853 Å
length_c	59.860 Å
angle_alpha	90.00 °
angle_beta	90.71 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.990 Å
resolution_low	48.970 Å
r_factor	0.1805
r_work	0.1787
r_free	0.2153

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

Single-chain Fv antibody of C6

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