Structure of a native Drosophila melanogaster hexameric nucleosome

条目编号 entry_id	9mu5
沉积日期 deposition_date	2025-01-13
最后修订 last_revision	2025-02-19
结构标题 title	Structure of a native Drosophila melanogaster hexameric nucleosome
关键词 keywords	Nucleosome, histones, histone, chromatin, DNA, GENE REGULATION; GENE REGULATION
实验方法 method	ELECTRON MICROSCOPY

回转半径 Rg (Guinier) rg_guinier	43.91 Å
回转半径 Rg (电子) rg_electron	41.30 Å
零角强度 I(0) i0	584609000.00
分子量 molecular_weight	142340.0 kDa
排除体积 excluded_volume	154960 ų
包络体积 envelope_volume	255650 ų
水化壳体积 shell_volume	53657 ų
包络直径 envelope_diameter	188.2 Å
壳层 Rg shell_rg	44.20 Å
包络 Rg envelope_rg	42.07 Å
形状 Rg shape_rg	41.10 Å
总 Rg total_rg	41.85 Å
总原子数 total_atoms	9666
残基数 n_residues	798
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å−1
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/ų
壳层衬度 contrast_shell	0.0300 e/ų
CRYSOL 版本 crysol_version	4.1.3

最大尺寸 Dmax dmax	174.6 Å
Rg (实空间) rg_real	44.06 Å
Rg 误差 (实空间) rg_real_error	2.12 Å
I(0) (实空间) i0_real	5.8460e+08
I(0) 误差 (实空间) i0_real_error	1.1200e+07
Rg (倒空间) rg_reciprocal	43.91 Å
I(0) (倒空间) i0_reciprocal	584500000.0000
解质量估计 total_estimate	0.8070
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	48.5 Å
偏度 Skewness skewness	0.470
峰度 Kurtosis kurtosis	0.200
角度范围 angular_range	— – 0.1800 Å−1
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	21830000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.565; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.950

冷冻电镜 EM 3D

分辨率 resolution	6.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	38738

Files (7)

• pr_distribution /app/data/pr_computation/mu/9mu5/pr_distribution.json
• pr_output /app/data/pr_computation/mu/9mu5/9mu5.pr.out
• pr_plot /app/data/visualization/pr_computation/mu/9mu5/9mu5_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/mu/9mu5/9mu5.dat
• saxs_fit /app/data/saxs_computation/mu/9mu5/9mu5.fit
• saxs_log /app/data/saxs_computation/mu/9mu5/9mu5.log
• saxs_plot /app/data/visualization/saxs_computation/mu/9mu5/9mu5_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/mu/9mu5/9mu5.fit
pddf	/app/data/pr_computation/mu/9mu5/9mu5.pr.out
profile	/app/data/saxs_computation/mu/9mu5/9mu5.dat