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9rm3

Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 17

Method: X-RAY DIFFRACTION D_max: 171.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rm3
deposition_date	2025-06-17
last_revision	2026-01-28
title	Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 17
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	44.55 Å
rg_electron	44.71 Å
i0	563385000.00
molecular_weight	127840.0 kDa
excluded_volume	123320 Å³
envelope_volume	261970 Å³
shell_volume	55079 Å³
envelope_diameter	177.8 Å
shell_rg	42.77 Å
envelope_rg	44.92 Å
shape_rg	44.67 Å
total_rg	44.69 Å
total_atoms	9650
n_residues	1160
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	171.6 Å
rg_real	44.95 Å
rg_real_error	2.64 Å
i0_real	5.6340e+08
i0_real_error	1.3550e+07
rg_reciprocal	44.56 Å
i0_reciprocal	563100000.0000
total_estimate	0.7970
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.0 Å
skewness	0.629
kurtosis	0.281
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	16210000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.550; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.934

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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	9650

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	man
entity_count	4

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	;(2R,4S,5R,6R)-5-acetamido-2-[[(2R,3R,4S,5R,6S)-6-[(2R,3S,4R,5R,6R)-5-acetamido-6-(2-azanylethoxy)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methoxy]-6-[(1R,2R)-1,2-bis(oxidanyl)-3-[(3-phenoxyphenyl)carbonylamino]propyl]-4-oxidanyl-oxane-2-carboxylic acid ;
formula_weight	912.9 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	97.256 Å
length_b	114.081 Å
length_c	155.274 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.857 Å
resolution_low	49.202 Å
r_factor	0.2441
r_work	0.2418
r_free	0.2893

fit	/app/data/saxs_computation/rm/9rm3/9rm3.fit
pddf	/app/data/pr_computation/rm/9rm3/9rm3.pr.out
profile	/app/data/saxs_computation/rm/9rm3/9rm3.dat

Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 17

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