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1eqz

X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 121.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1eqz
deposition_date	2000-04-06
title	X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION
keywords	;NUCLEOSOME, NUCLEOSOME CORE PARTICLE, HISTONE, MICROGRAVITY HISTONE OCTAMER, DNA PALINDROME, DNA PROTEIN COMPLEX, CHROMATIN, CHROMOSOMAL PROTEIN, HISTONE FOLD, BENT DNA, STRUCTURAL PROTEIN-DNA COMPLEX ;; STRUCTURAL PROTEIN/DNA
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	40.60 Å
rg_electron	38.44 Å
i0	923168000.00
molecular_weight	189250.0 kDa
excluded_volume	211760 Å³
envelope_volume	320510 Å³
shell_volume	66781 Å³
envelope_diameter	136.8 Å
shell_rg	46.27 Å
envelope_rg	38.56 Å
shape_rg	38.28 Å
total_rg	39.15 Å
total_atoms	12870
n_residues	1165
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	121.6 Å
rg_real	40.42 Å
rg_real_error	0.77 Å
i0_real	9.2320e+08
i0_real_error	1.5130e+07
rg_reciprocal	40.60 Å
i0_reciprocal	923300000.0000
total_estimate	0.8362
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.8 Å
skewness	0.099
kurtosis	-0.655
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	85010000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	146 NUCLEOTIDES LONG DNA
formula_weight	45054.8 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	I,J
atom_count	13325

ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT

Entity 2 polymer

description	PROTEIN (HISTONE H2A)
formula_weight	13969.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E

MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTDSHKAKAK

Entity 3 polymer

description	PROTEIN (HISTONE H2B)
formula_weight	13953.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MPEPAKSAPAPKKGSKKAVTKTQKKGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Entity 4 polymer

description	PROTEIN (HISTONE H3)
formula_weight	15421.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Entity 5 polymer

description	PROTEIN (HISTONE H4)
formula_weight	11394.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Entity 6 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	7

Entity 7 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	15

Entity 8 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	CACODYLATE ION
formula_weight	137.0 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	349

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6. Citations (3)

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length_a	105.280 Å
length_b	109.710 Å
length_c	181.120 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.500 Å
resolution_low	25.340 Å
r_factor	0.2190
r_work	0.2190
r_free	0.2820

fit	/app/data/saxs_computation/eq/1eqz/1eqz.fit
pddf	/app/data/pr_computation/eq/1eqz/1eqz.pr.out
profile	/app/data/saxs_computation/eq/1eqz/1eqz.dat

X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION

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

Diffraction

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (3)

7. Files & Curves (10)

Files (7)

Curves (3)