Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom

entry_id	9xsf
deposition_date	2025-11-20
title	Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom
keywords	nucleosome, H4S47, GlcNAc, NUCLEAR PROTEIN; NUCLEAR PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	38.34 Å
rg_electron	35.53 Å
i0	579914000.00
molecular_weight	148010.0 kDa
excluded_volume	165280 ų
envelope_volume	243480 ų
shell_volume	56492 ų
envelope_diameter	110.2 Å
shell_rg	42.76 Å
envelope_rg	34.88 Å
shape_rg	35.36 Å
total_rg	36.29 Å
total_atoms	10112
n_residues	911
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	110.6 Å
rg_real	38.09 Å
rg_real_error	0.60 Å
i0_real	5.7990e+08
i0_real_error	9.3370e+06
rg_reciprocal	38.25 Å
i0_reciprocal	580000000.0000
total_estimate	0.8426
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.9 Å
skewness	0.087
kurtosis	-0.623
angular_range	— – 0.2050 Å−1
current_alpha	0.0000
highest_alpha	21780000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.986; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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	3.390 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	3.39 Å
resolution_method	—
num_particles	275466

Files (7)

• pr_distribution /app/data/pr_computation/xs/9xsf/pr_distribution.json
• pr_output /app/data/pr_computation/xs/9xsf/9xsf.pr.out
• pr_plot /app/data/visualization/pr_computation/xs/9xsf/9xsf_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/xs/9xsf/9xsf.dat
• saxs_fit /app/data/saxs_computation/xs/9xsf/9xsf.fit
• saxs_log /app/data/saxs_computation/xs/9xsf/9xsf.log
• saxs_plot /app/data/visualization/saxs_computation/xs/9xsf/9xsf_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/xs/9xsf/9xsf.fit
pddf	/app/data/pr_computation/xs/9xsf/9xsf.pr.out
profile	/app/data/saxs_computation/xs/9xsf/9xsf.dat