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9udp

Single-chain Fv antibody of B2

Method: X-RAY DIFFRACTION D_max: 57.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9udp
deposition_date	2025-04-07
title	Single-chain Fv antibody of B2
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	18.23 Å
rg_electron	17.20 Å
i0	11572400.00
molecular_weight	25196.0 kDa
excluded_volume	31434 Å³
envelope_volume	35277 Å³
shell_volume	17233 Å³
envelope_diameter	58.1 Å
shell_rg	23.18 Å
envelope_rg	17.46 Å
shape_rg	17.13 Å
total_rg	18.33 Å
total_atoms	1776
n_residues	229
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	57.0 Å
rg_real	18.14 Å
rg_real_error	0.28 Å
i0_real	1.1570e+07
i0_real_error	1.3900e+05
rg_reciprocal	18.16 Å
i0_reciprocal	11570000.0000
total_estimate	0.9014
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	23.1 Å
skewness	0.195
kurtosis	-0.409
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	3959000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.992

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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 B2
formula_weight	25803.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2167

GSQAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGGGGGSGGGGSGGGGSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYLMHWVKQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQFSSLTSEDSAVYYCARYYYGAYFDYWGQGTTLTVSS

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	223

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6. Citations (1)

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length_a	39.762 Å
length_b	71.956 Å
length_c	81.289 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	1.480 Å
resolution_low	31.990 Å
r_factor	0.1565
r_work	0.1556
r_free	0.1743

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

Single-chain Fv antibody of B2

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