SAXSdb — 9qik

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1. Structure Basics

entry_id	9qik
deposition_date	2025-03-17
title	M2 nucleosome
keywords	NCP, chromatin remodeling, TRANSLOCASE; TRANSLOCASE
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	39.09 Å
rg_electron	36.32 Å
i0	692238000.00
molecular_weight	160120.0 kDa
excluded_volume	177590 Å³
envelope_volume	261320 Å³
shell_volume	58719 Å³
envelope_diameter	116.7 Å
shell_rg	43.77 Å
envelope_rg	35.75 Å
shape_rg	36.14 Å
total_rg	37.07 Å
total_atoms	10927
n_residues	966
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	111.4 Å
rg_real	38.84 Å
rg_real_error	0.62 Å
i0_real	6.9220e+08
i0_real_error	1.1710e+07
rg_reciprocal	39.00 Å
i0_reciprocal	692300000.0000
total_estimate	0.6501
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	44.6 Å
skewness	0.096
kurtosis	-0.668
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	37720000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.994; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.991; Smooth: 0.287

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Histone H2A type 1
formula_weight	13993.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10927

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKKTESAKSAKSK

Source

organism	Xenopus laevis laevis
ncbi_taxonomy_id	443947
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H2B 1.1
formula_weight	13965.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Xenopus laevis laevis
ncbi_taxonomy_id	443947
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H3
formula_weight	15361.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

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

Entity 4 polymer

description	Histone H4
formula_weight	11394.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Xenopus laevis laevis
ncbi_taxonomy_id	443947
host_organism	Escherichia coli

Entity 5 polymer

description	DNA (220-MER)
formula_weight	68160.4 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

TTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTCGAGCTCGGTACTCGGGTTCAATACATGCATGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTTGCTACTAGTCTCCAGGCACGTGTCAGATATATACATCCTGGGGCG

Source

organism	Xenopus laevis laevis
ncbi_taxonomy_id	443947
host_organism	Escherichia coli

Entity 6 polymer

description	DNA (220-MER)
formula_weight	67698.1 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

CGCCCCAGGATGTATATATCTGACACGTGCCTGGAGACTAGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCATGCATGTATTGAACCCGAGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAA

Source

organism	Xenopus laevis laevis
ncbi_taxonomy_id	443947
host_organism	Escherichia coli

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6. Citations (1)

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resolution	3.030 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.03 Å
resolution_method	—
num_particles	93970

fit	/app/data/saxs_computation/qi/9qik/9qik.fit
pddf	/app/data/pr_computation/qi/9qik/9qik.pr.out
profile	/app/data/saxs_computation/qi/9qik/9qik.dat

M2 nucleosome

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

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

Source

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)