Structure of a native Drosophila melanogaster octameric nucleosome

条目编号 entry_id	9mu4
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 octameric 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	43.07 Å
回转半径 Rg (电子) rg_electron	40.34 Å
零角强度 I(0) i0	968651000.00
分子量 molecular_weight	187900.0 kDa
排除体积 excluded_volume	206840 ų
包络体积 envelope_volume	323960 ų
水化壳体积 shell_volume	66234 ų
包络直径 envelope_diameter	151.4 Å
壳层 Rg shell_rg	46.62 Å
包络 Rg envelope_rg	40.47 Å
形状 Rg shape_rg	40.16 Å
总 Rg total_rg	40.99 Å
总原子数 total_atoms	12794
残基数 n_residues	1098
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	141.0 Å
Rg (实空间) rg_real	43.01 Å
Rg 误差 (实空间) rg_real_error	1.25 Å
I(0) (实空间) i0_real	9.6860e+08
I(0) 误差 (实空间) i0_real_error	1.8670e+07
Rg (倒空间) rg_reciprocal	43.07 Å
I(0) (倒空间) i0_reciprocal	968700000.0000
解质量估计 total_estimate	0.6586
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	49.5 Å
偏度 Skewness skewness	0.293
峰度 Kurtosis kurtosis	-0.262
角度范围 angular_range	— – 0.1850 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	73240000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 0.083; Positv: 1.000; Valcen: 0.993; Smooth: 0.679

晶胞参数 Unit Cell

晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

对称性 Symmetry

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

冷冻电镜 EM 3D

分辨率 resolution	3.29 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	66988

Files (7)

• pr_distribution /app/data/pr_computation/mu/9mu4/pr_distribution.json
• pr_output /app/data/pr_computation/mu/9mu4/9mu4.pr.out
• pr_plot /app/data/visualization/pr_computation/mu/9mu4/9mu4_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/mu/9mu4/9mu4.dat
• saxs_fit /app/data/saxs_computation/mu/9mu4/9mu4.fit
• saxs_log /app/data/saxs_computation/mu/9mu4/9mu4.log
• saxs_plot /app/data/visualization/saxs_computation/mu/9mu4/9mu4_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/mu/9mu4/9mu4.fit
pddf	/app/data/pr_computation/mu/9mu4/9mu4.pr.out
profile	/app/data/saxs_computation/mu/9mu4/9mu4.dat