Adaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of tissue-extracted NC1 hexamer

条目编号 entry_id	8tys
沉积日期 deposition_date	2023-08-25
结构标题 title	Adaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of tissue-extracted NC1 hexamer
关键词 keywords	collagen IV, trimerization domain, hexamer assembly, basement membrane, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	31.10 Å
回转半径 Rg (电子) rg_electron	30.12 Å
零角强度 I(0) i0	387905000.00
分子量 molecular_weight	149940.0 kDa
排除体积 excluded_volume	183910 ų
包络体积 envelope_volume	216580 ų
水化壳体积 shell_volume	55606 ų
包络直径 envelope_diameter	98.8 Å
壳层 Rg shell_rg	40.15 Å
包络 Rg envelope_rg	30.19 Å
形状 Rg shape_rg	30.08 Å
总 Rg total_rg	30.98 Å
总原子数 total_atoms	10472
残基数 n_residues	1352
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	97.2 Å
Rg (实空间) rg_real	30.88 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	3.8790e+08
I(0) 误差 (实空间) i0_real_error	5.4440e+06
Rg (倒空间) rg_reciprocal	30.98 Å
I(0) (倒空间) i0_reciprocal	387900000.0000
解质量估计 total_estimate	0.6676
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	40.0 Å
偏度 Skewness skewness	0.164
峰度 Kurtosis kurtosis	-0.401
角度范围 angular_range	— – 0.2550 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	225700000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 0.040; Positv: 1.000; Valcen: 0.982; Smooth: 0.952

晶胞参数 Unit Cell

晶胞边长 a length_a	145.209 Å
晶胞边长 b length_b	145.209 Å
晶胞边长 c length_c	106.491 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	120.00 °
晶胞分子数 Z z_pdb	24

对称性 Symmetry

空间群 space_group	P 63
空间群编号 int_tables_number	173
晶系 crystal_system	hexagonal

精修参数 Refinement

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	40.630 Å
R 因子 r_factor	0.2428
R_work r_work	0.2411
R_free r_free	0.2773

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/ty/8tys/pr_distribution.json
• pr_output /app/data/pr_computation/ty/8tys/8tys.pr.out
• pr_plot /app/data/visualization/pr_computation/ty/8tys/8tys_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/ty/8tys/8tys.dat
• saxs_fit /app/data/saxs_computation/ty/8tys/8tys.fit
• saxs_log /app/data/saxs_computation/ty/8tys/8tys.log
• saxs_plot /app/data/visualization/saxs_computation/ty/8tys/8tys_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/ty/8tys/8tys.fit
pddf	/app/data/pr_computation/ty/8tys/8tys.pr.out
profile	/app/data/saxs_computation/ty/8tys/8tys.dat