Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement)

entry_id	9y46
deposition_date	2025-09-02
title	Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement)
keywords	Nucleosome, chromatin, DNA, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	41.42 Å
rg_electron	38.66 Å
i0	835281000.00
molecular_weight	176360.0 kDa
excluded_volume	195640 ų
envelope_volume	309400 ų
shell_volume	65328 ų
envelope_diameter	122.4 Å
shell_rg	45.94 Å
envelope_rg	37.81 Å
shape_rg	38.49 Å
total_rg	39.37 Å
total_atoms	12033
n_residues	1057
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	116.1 Å
rg_real	41.22 Å
rg_real_error	0.71 Å
i0_real	8.3530e+08
i0_real_error	1.2300e+07
rg_reciprocal	41.42 Å
i0_reciprocal	835500000.0000
total_estimate	0.6343
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	48.9 Å
skewness	0.063
kurtosis	-0.710
angular_range	— – 0.1900 Å−1
current_alpha	0.0000
highest_alpha	62400000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.996; Stabil: 0.999; Sysdev: 0.046; Positv: 1.000; Valcen: 1.000; Smooth: 0.121

Unit Cell

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	—

Symmetry

space_group	P 1
int_tables_number	1
crystal_system	—

Refinement

resolution	2.590 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	2.59 Å
resolution_method	—
num_particles	182456

Files (7)

• pr_distribution /app/data/pr_computation/y4/9y46/pr_distribution.json
• pr_output /app/data/pr_computation/y4/9y46/9y46.pr.out
• pr_plot /app/data/visualization/pr_computation/y4/9y46/9y46_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/y4/9y46/9y46.dat
• saxs_fit /app/data/saxs_computation/y4/9y46/9y46.fit
• saxs_log /app/data/saxs_computation/y4/9y46/9y46.log
• saxs_plot /app/data/visualization/saxs_computation/y4/9y46/9y46_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/y4/9y46/9y46.fit
pddf	/app/data/pr_computation/y4/9y46/9y46.pr.out
profile	/app/data/saxs_computation/y4/9y46/9y46.dat