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9rgi

X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein is treated 6 days with [VIVO(acac)2]

Method: X-RAY DIFFRACTION D_max: 69.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rgi
deposition_date	2025-06-06
last_revision	2025-12-03
title	X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein is treated 6 days with [VIVO(acac)2]
keywords	human ferritin, vanadium, polyoxometalate, pentadecavanadate, METAL TRANSPORT; METAL TRANSPORT
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	20.25 Å
rg_electron	19.55 Å
i0	17954400.00
molecular_weight	20538.0 kDa
excluded_volume	19181 Å³
envelope_volume	31348 Å³
shell_volume	14913 Å³
envelope_diameter	70.5 Å
shell_rg	23.89 Å
envelope_rg	19.50 Å
shape_rg	19.05 Å
total_rg	20.75 Å
total_atoms	1487
n_residues	174
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	69.3 Å
rg_real	20.44 Å
rg_real_error	0.61 Å
i0_real	1.7950e+07
i0_real_error	2.3380e+05
rg_reciprocal	20.41 Å
i0_reciprocal	17950000.0000
total_estimate	0.8356
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	18.8 Å
skewness	0.569
kurtosis	-0.257
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	1449000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.707; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.763; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Ferritin heavy chain
formula_weight	21124.5 kDa
ec_number	1.16.3.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AAA
atom_count	1821

TTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDNES

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	Polyoxidovanadate complex
formula_weight	1340.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	244

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6. Citations (1)

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length_a	183.280 Å
length_b	183.280 Å
length_c	183.280 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	96

space_group	F 4 3 2
int_tables_number	209
crystal_system	—

resolution	1.543 Å
resolution_low	91.808 Å
r_factor	—
r_work	0.1762
r_free	0.1979

fit	/app/data/saxs_computation/rg/9rgi/9rgi.fit
pddf	/app/data/pr_computation/rg/9rgi/9rgi.pr.out
profile	/app/data/saxs_computation/rg/9rgi/9rgi.dat