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9ro7

Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 7-012

Method: X-RAY DIFFRACTION D_max: 170.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ro7
deposition_date	2025-06-20
last_revision	2025-12-10
title	Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 7-012
keywords	Siglec, sialic acid, B cell, 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	43.62 Å
rg_electron	43.79 Å
i0	591373000.00
molecular_weight	130890.0 kDa
excluded_volume	126170 Å³
envelope_volume	262760 Å³
shell_volume	55749 Å³
envelope_diameter	181.8 Å
shell_rg	42.54 Å
envelope_rg	44.69 Å
shape_rg	43.76 Å
total_rg	43.80 Å
total_atoms	9883
n_residues	1194
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	170.7 Å
rg_real	44.01 Å
rg_real_error	2.62 Å
i0_real	5.9140e+08
i0_real_error	1.2630e+07
rg_reciprocal	43.62 Å
i0_reciprocal	591100000.0000
total_estimate	0.7869
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	47.4 Å
skewness	0.651
kurtosis	0.315
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	19270000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.502; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.944

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	B-cell receptor CD22
formula_weight	36660.3 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	9883

ETGDSSKWVFEHPETLYAWEGACVWIPCTYRALDGDLESFILFHNPEYNKATSKFDGTRLYESTKDGKVPSEQKRVQFLGDKNKNCTLSIHPVHLADSGQLGLRMESKTEKWMERIHLAVSERPFPPHIQLPPEIQESQEVTLTCLLAFSCYGYPIQLQWLLEGVPMRQAAVTSTSLTIKSVFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSADTVQLNVKHTPKLEIKVTPSDAIVREGDSVTMTCEVSSSNPEYTTVSWLKDGTSLKKQNTFTLNLREVTKDQSGKYCCQVSNDVGPGRSEEVFLQVQYAGGTKHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	;(2R,4S,5R,6R)-5-acetamido-6-[(1S,2S)-1,2-bis(oxidanyl)-3-[(4-phenylphenyl)carbonylamino]propyl]-2-[[1-[(2R)-3-(2-methyl-5-nitro-imidazol-1-yl)-2-oxidanyl-propyl]-1,2,3-triazol-4-yl]methyl]-4-oxidanyl-oxane-2-carboxylic acid ;
formula_weight	736.7 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

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6. Citations (1)

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length_a	102.395 Å
length_b	113.294 Å
length_c	138.367 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.150 Å
resolution_low	39.425 Å
r_factor	0.2420
r_work	0.2391
r_free	0.2977

fit	/app/data/saxs_computation/ro/9ro7/9ro7.fit
pddf	/app/data/pr_computation/ro/9ro7/9ro7.pr.out
profile	/app/data/saxs_computation/ro/9ro7/9ro7.dat

Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 7-012

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