SAXSdb — 10yb

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1. Structure Basics

entry_id	10yb
deposition_date	2026-02-12
title	Nucleosome containing a nick at SHL-2
keywords	Nucleosome, DNA Ligase IIIa, DNA Repair, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	40.36 Å
rg_electron	37.60 Å
i0	826070000.00
molecular_weight	174550.0 kDa
excluded_volume	193080 Å³
envelope_volume	291320 Å³
shell_volume	62839 Å³
envelope_diameter	119.8 Å
shell_rg	45.17 Å
envelope_rg	37.07 Å
shape_rg	37.43 Å
total_rg	38.32 Å
total_atoms	11904
n_residues	1036
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	120.1 Å
rg_real	40.17 Å
rg_real_error	0.97 Å
i0_real	8.2610e+08
i0_real_error	1.5050e+07
rg_reciprocal	40.36 Å
i0_reciprocal	826200000.0000
total_estimate	0.9035
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	46.2 Å
skewness	0.071
kurtosis	-0.702
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	58110000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.851

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Histone H3.2
formula_weight	15257.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	11904

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H4
formula_weight	11263.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H2A type 1
formula_weight	13990.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2B type 1-C/E/F/G/I
formula_weight	13806.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	601 I strand (non-damaged strand)
formula_weight	45138.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT

Entity 6 polymer

description	601 J strand (damaged strand 1)
formula_weight	17352.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGG

Entity 7 polymer

description	601 K strand (damaged strand 2)
formula_weight	28213.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	K

TTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

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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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	50482

fit	/app/data/saxs_computation/0y/10yb/10yb.fit
pddf	/app/data/pr_computation/0y/10yb/10yb.pr.out
profile	/app/data/saxs_computation/0y/10yb/10yb.dat

Nucleosome containing a nick at SHL-2

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 (7)

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

Entity 7 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)