Crystal Structure of the Complex of Side-VI IG1 Domain and Beat-Vc IG1+2 Domains

条目编号 entry_id	9nsf
沉积日期 deposition_date	2025-03-16
最后修订 last_revision	2026-06-10
结构标题 title	Crystal Structure of the Complex of Side-VI IG1 Domain and Beat-Vc IG1+2 Domains
关键词 keywords	Immunoglobulin Superfamily, Glycoprotein, Complex, Cell Surface Receptor, CELL ADHESION; CELL ADHESION
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	37.67 Å
回转半径 Rg (电子) rg_electron	38.54 Å
零角强度 I(0) i0	102209000.00
分子量 molecular_weight	79975.0 kDa
排除体积 excluded_volume	99809 ų
包络体积 envelope_volume	136020 ų
水化壳体积 shell_volume	34211 ų
包络直径 envelope_diameter	161.1 Å
壳层 Rg shell_rg	37.26 Å
包络 Rg envelope_rg	39.63 Å
形状 Rg shape_rg	38.55 Å
总 Rg total_rg	38.41 Å
总原子数 total_atoms	5628
残基数 n_residues	694
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	154.3 Å
Rg (实空间) rg_real	38.34 Å
Rg 误差 (实空间) rg_real_error	2.59 Å
I(0) (实空间) i0_real	1.0220e+08
I(0) 误差 (实空间) i0_real_error	1.9490e+06
Rg (倒空间) rg_reciprocal	37.91 Å
I(0) (倒空间) i0_reciprocal	102200000.0000
解质量估计 total_estimate	0.7430
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	44.1 Å
偏度 Skewness skewness	0.758
峰度 Kurtosis kurtosis	0.668
角度范围 angular_range	— – 0.2100 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8656000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.434; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.474; Smooth: 0.879

晶胞参数 Unit Cell

晶胞边长 a length_a	87.480 Å
晶胞边长 b length_b	87.480 Å
晶胞边长 c length_c	387.379 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	12

对称性 Symmetry

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	hexagonal

精修参数 Refinement

分辨率 resolution	3.930 Å
最低分辨率 resolution_low	49.140 Å
R 因子 r_factor	0.2363
R_work r_work	0.2338
R_free r_free	0.2837

衍射实验 Diffraction

实验温度 temperature

120.0 K

Files (7)

• pr_distribution /app/data/pr_computation/ns/9nsf/pr_distribution.json
• pr_output /app/data/pr_computation/ns/9nsf/9nsf.pr.out
• pr_plot /app/data/visualization/pr_computation/ns/9nsf/9nsf_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/ns/9nsf/9nsf.dat
• saxs_fit /app/data/saxs_computation/ns/9nsf/9nsf.fit
• saxs_log /app/data/saxs_computation/ns/9nsf/9nsf.log
• saxs_plot /app/data/visualization/saxs_computation/ns/9nsf/9nsf_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/ns/9nsf/9nsf.fit
pddf	/app/data/pr_computation/ns/9nsf/9nsf.pr.out
profile	/app/data/saxs_computation/ns/9nsf/9nsf.dat