Single-chain Fv antibody of B2 complex with NP-glycine

Method: X-RAY DIFFRACTION D_max: 56.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9udr
deposition_date	2025-04-07
title	Single-chain Fv antibody of B2 complex with NP-glycine
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	17.17 Å
i0	11502900.00
molecular_weight	25093.0 kDa
excluded_volume	31283 Å³
envelope_volume	35011 Å³
shell_volume	17141 Å³
envelope_diameter	55.6 Å
shell_rg	23.14 Å
envelope_rg	17.40 Å
shape_rg	17.11 Å
total_rg	18.28 Å
total_atoms	1771
n_residues	230
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	56.0 Å
rg_real	18.14 Å
rg_real_error	0.24 Å
i0_real	1.1500e+07
i0_real_error	1.3310e+05
rg_reciprocal	18.15 Å
i0_reciprocal	11500000.0000
total_estimate	0.9053
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	23.5 Å
skewness	0.185
kurtosis	-0.437
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	3604000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (1)

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length_a	40.039 Å
length_b	71.834 Å
length_c	82.054 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	1.340 Å
resolution_low	41.030 Å
r_factor	0.1512
r_work	0.1506
r_free	0.1632

description	Single-chain Fv antibody of B2
formula_weight	25803.5 kDa
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2256

Single-chain Fv antibody of B2 complex with NP-glycine

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

description	N-[(4-hydroxy-3-nitrophenyl)acetyl]glycine
formula_weight	254.2 kDa
src_method	syn
entity_count	1

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	279

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