Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2

entry_id	9zen
deposition_date	2025-11-30
title	Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2
keywords	chromatin, nucleosome, VHH, antibody, acidic-patch, AP, DE NOVO PROTEIN; DE NOVO PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	42.34 Å
rg_electron	40.39 Å
i0	1019110000.00
molecular_weight	200650.0 kDa
excluded_volume	225440 ų
envelope_volume	349100 ų
shell_volume	70475 ų
envelope_diameter	154.1 Å
shell_rg	47.25 Å
envelope_rg	39.75 Å
shape_rg	40.29 Å
total_rg	40.90 Å
total_atoms	13745
n_residues	1288
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	141.7 Å
rg_real	42.07 Å
rg_real_error	1.17 Å
i0_real	1.0190e+09
i0_real_error	1.7550e+07
rg_reciprocal	42.33 Å
i0_reciprocal	1019000000.0000
total_estimate	0.8771
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	53.6 Å
skewness	0.033
kurtosis	-0.569
angular_range	— – 0.1850 Å−1
current_alpha	0.0000
highest_alpha	67550000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.994

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	3.170 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	3.17 Å
resolution_method	—
num_particles	276423

Files (7)

• pr_distribution /app/data/pr_computation/ze/9zen/pr_distribution.json
• pr_output /app/data/pr_computation/ze/9zen/9zen.pr.out
• pr_plot /app/data/visualization/pr_computation/ze/9zen/9zen_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/ze/9zen/9zen.dat
• saxs_fit /app/data/saxs_computation/ze/9zen/9zen.fit
• saxs_log /app/data/saxs_computation/ze/9zen/9zen.log
• saxs_plot /app/data/visualization/saxs_computation/ze/9zen/9zen_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/ze/9zen/9zen.fit
pddf	/app/data/pr_computation/ze/9zen/9zen.pr.out
profile	/app/data/saxs_computation/ze/9zen/9zen.dat