SAXSdb — 9px5

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1. Structure Basics

entry_id	9px5
deposition_date	2025-08-05
last_revision	2025-09-10
title	Crystal structure of Fab 7268 in complex with MBP-TREM2 Ig domain fusion
keywords	Fab, 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	34.97 Å
rg_electron	34.60 Å
i0	141194000.00
molecular_weight	93406.0 kDa
excluded_volume	115880 Å³
envelope_volume	156500 Å³
shell_volume	39487 Å³
envelope_diameter	116.5 Å
shell_rg	39.48 Å
envelope_rg	34.32 Å
shape_rg	34.58 Å
total_rg	35.03 Å
total_atoms	6597
n_residues	903
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	115.5 Å
rg_real	35.11 Å
rg_real_error	1.23 Å
i0_real	1.4120e+08
i0_real_error	2.5490e+06
rg_reciprocal	35.02 Å
i0_reciprocal	141200000.0000
total_estimate	0.8725
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.9 Å
skewness	0.412
kurtosis	-0.539
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	20340000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.910

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Maltose/maltodextrin-binding periplasmic protein,Triggering receptor expressed on myeloid cells 2
formula_weight	54172.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6597

KTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAHDTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLADPLDHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	7268 Fab Heavy Chain
formula_weight	24081.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLQQWGAGLLKPSETLSLTCAVYGVSFSGYHWYWIRQPPGKGLEWIGEIDNKGQTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARGGSYYGHPYLAAPDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 polymer

description	7268 Fab Light Chain
formula_weight	23363.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 branched

description	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
formula_weight	342.3 kDa
src_method	nat
entity_count	1

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	119.900 Å
length_b	64.230 Å
length_c	160.800 Å
angle_alpha	90.00 °
angle_beta	94.45 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	3.700 Å
resolution_low	47.050 Å
r_factor	0.2489
r_work	0.2480
r_free	0.2682

fit	/app/data/saxs_computation/px/9px5/9px5.fit
pddf	/app/data/pr_computation/px/9px5/9px5.pr.out
profile	/app/data/saxs_computation/px/9px5/9px5.dat

Crystal structure of Fab 7268 in complex with MBP-TREM2 Ig domain fusion

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 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)