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9zd5

Human Stomatin - intramembrane region

Method: ELECTRON MICROSCOPY D_max: 105.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zd5
deposition_date	2025-11-24
title	Human Stomatin - intramembrane region
keywords	Oligomer, C8 symmetry, scaffold, MEMBRANE PROTEIN, intramembrane region; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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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	32.98 Å
rg_electron	33.75 Å
i0	103468000.00
molecular_weight	90171.0 kDa
excluded_volume	116960 Å³
envelope_volume	154930 Å³
shell_volume	37926 Å³
envelope_diameter	120.6 Å
shell_rg	40.58 Å
envelope_rg	33.82 Å
shape_rg	33.72 Å
total_rg	34.50 Å
total_atoms	6340
n_residues	776
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	105.4 Å
rg_real	33.04 Å
rg_real_error	0.77 Å
i0_real	1.0350e+08
i0_real_error	1.5400e+06
rg_reciprocal	33.02 Å
i0_reciprocal	103500000.0000
total_estimate	0.8972
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.3 Å
skewness	0.311
kurtosis	-0.484
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	22380000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.857

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Stomatin
formula_weight	21128.7 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	I,E,G,H
atom_count	6340

XXXXXXXXXXXXXXXXXXKGLGPCGWILVAFSFLFTVITFPISIWMCIKIIKEYERAIIFRLGRILQGGAKGPGLFFILPCTDSFIKVDMRTISFDIPPQEILTKDSVTISVDGVVYYRVQNATLAVANITNADSATRLLAQTTLRNVLGTKNLSQILSDREEIAHNMQSTLDDATDAWGIKVERVEIKDVKLP

Entity 2 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	nat
entity_count	12

Entity 3 non-polymer

description	DIUNDECYL PHOSPHATIDYL CHOLINE
formula_weight	622.8 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
formula_weight	379.5 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.20 Å
resolution_method	—
num_particles	2151648

fit	/app/data/saxs_computation/zd/9zd5/9zd5.fit
pddf	/app/data/pr_computation/zd/9zd5/9zd5.pr.out
profile	/app/data/saxs_computation/zd/9zd5/9zd5.dat