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9y0d

Crystal structure of human IgE Fab 2H22

Method: X-RAY DIFFRACTION D_max: 78.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y0d
deposition_date	2025-08-28
title	Crystal structure of human IgE Fab 2H22
keywords	allergen, IgE, IgE Fab, allergen-antibody complex, 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	25.43 Å
rg_electron	24.43 Å
i0	35993800.00
molecular_weight	46169.0 kDa
excluded_volume	57626 Å³
envelope_volume	71224 Å³
shell_volume	24471 Å³
envelope_diameter	81.9 Å
shell_rg	31.40 Å
envelope_rg	24.20 Å
shape_rg	24.41 Å
total_rg	25.26 Å
total_atoms	3255
n_residues	437
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	78.9 Å
rg_real	25.40 Å
rg_real_error	0.45 Å
i0_real	3.5990e+07
i0_real_error	4.8580e+05
rg_reciprocal	25.41 Å
i0_reciprocal	35990000.0000
total_estimate	0.9145
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.0 Å
skewness	0.251
kurtosis	-0.572
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	4883000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	hIgE Fab 2H22 heavy chain
formula_weight	23953.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3422

EVQLQESGPGLVKPSETLSLTCTVSGGSISTNGYYWGWIRQPPGKGLDWIGSISYSGNTYYNPSLQSRVSISVDTSKKQFSLKLSSVTASDTAVYYCARHGANWEGVVGWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 polymer

description	hIgE Fab 2H22 light chain
formula_weight	22630.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QSVLPQPPSVSAAPGQNVTISCSGSISNIGNNYVSWYQRLPGTAPKLLIYGNNNRPSGIPDRFSGSKSATSATLGITGLQAGDEAVYYCGTWDSSLRAGVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	167

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6. Citations (1)

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length_a	116.769 Å
length_b	116.769 Å
length_c	71.102 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 65
int_tables_number	170
crystal_system	—

resolution	2.270 Å
resolution_low	27.019 Å
r_factor	—
r_work	0.1870
r_free	0.2435

fit	/app/data/saxs_computation/y0/9y0d/9y0d.fit
pddf	/app/data/pr_computation/y0/9y0d/9y0d.pr.out
profile	/app/data/saxs_computation/y0/9y0d/9y0d.dat

Crystal structure of human IgE Fab 2H22

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)