SAXSdb — 9w74

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1. Structure Basics

entry_id	9w74
deposition_date	2025-08-05
title	Cryo-EM structure of the close-packed di-hexasome (CPDH)
keywords	Chromatin, Nucleosome, Hexasome, Subnucleosome, Histone, DNA, GENE REGULATION; GENE REGULATION
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	46.18 Å
rg_electron	43.67 Å
i0	1616340000.00
molecular_weight	252850.0 kDa
excluded_volume	283260 Å³
envelope_volume	445710 Å³
shell_volume	83410 Å³
envelope_diameter	154.4 Å
shell_rg	50.70 Å
envelope_rg	41.98 Å
shape_rg	43.52 Å
total_rg	44.25 Å
total_atoms	17263
n_residues	1513
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	144.3 Å
rg_real	45.84 Å
rg_real_error	0.85 Å
i0_real	1.6160e+09
i0_real_error	2.7790e+07
rg_reciprocal	46.18 Å
i0_reciprocal	1617000000.0000
total_estimate	0.8772
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.7 Å
skewness	0.078
kurtosis	-0.360
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	99900000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.882

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Histone H3.2
formula_weight	15435.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,E,K,O
atom_count	17263

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H4
formula_weight	13307.5 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,F,L,P

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGGSSGLVPRGSLEHHHHHH

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H2A type 1
formula_weight	18087.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,M

MKETAAAKFERQHMDSPDLHHHHHHGTLVPRGSMGMSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2B 1.1
formula_weight	13655.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,N

MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 5 polymer

description	DNA (207-MER)
formula_weight	64788.9 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 6 polymer

description	DNA (207-MER)
formula_weight	62922.8 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

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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	4.940 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.94 Å
resolution_method	—
num_particles	4963

fit	/app/data/saxs_computation/w7/9w74/9w74.fit
pddf	/app/data/pr_computation/w7/9w74/9w74.pr.out
profile	/app/data/saxs_computation/w7/9w74/9w74.dat

Cryo-EM structure of the close-packed di-hexasome (CPDH)

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)