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9sju

Cryo-EM structure of Human Apoferritin at pH 7

Method: ELECTRON MICROSCOPY D_max: 134.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sju
deposition_date	2025-09-01
title	Cryo-EM structure of Human Apoferritin at pH 7
keywords	Apoferritin, Ferritin, Metal storage, Low pH, METAL BINDING PROTEIN; METAL BINDING 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	53.76 Å
rg_electron	52.77 Å
i0	3586130000.00
molecular_weight	484840.0 kDa
excluded_volume	598790 Å³
envelope_volume	953740 Å³
shell_volume	147190 Å³
envelope_diameter	134.6 Å
shell_rg	63.48 Å
envelope_rg	47.62 Å
shape_rg	52.76 Å
total_rg	53.10 Å
total_atoms	34056
n_residues	4152
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	134.4 Å
rg_real	53.22 Å
rg_real_error	0.37 Å
i0_real	3.5860e+09
i0_real_error	5.2020e+07
rg_reciprocal	54.20 Å
i0_reciprocal	3591000000.0000
total_estimate	0.7981
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	88.1 Å
skewness	-0.391
kurtosis	-0.640
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	120300000000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.874; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ferritin heavy chain, N-terminally processed
formula_weight	20176.6 kDa
src_method	man
entity_count	24

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,V,W,X,Y
atom_count	35352

STSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLSEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	24

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	24

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1296

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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	2.08 Å
resolution_method	—
num_particles	432247

fit	/app/data/saxs_computation/sj/9sju/9sju.fit
pddf	/app/data/pr_computation/sj/9sju/9sju.pr.out
profile	/app/data/saxs_computation/sj/9sju/9sju.dat