Structure of Hailong HalB in complex with oligodeoxyadenylate

条目编号 entry_id	9dbh
沉积日期 deposition_date	2024-08-23
结构标题 title	Structure of Hailong HalB in complex with oligodeoxyadenylate
关键词 keywords	Hailong, nucleotidyltransferase, oligodeoxyadenylate, anti-phage defense, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-DNA complex; ANTIVIRAL PROTEIN/DNA
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	32.68 Å
回转半径 Rg (电子) rg_electron	31.72 Å
零角强度 I(0) i0	177901000.00
分子量 molecular_weight	102540.0 kDa
排除体积 excluded_volume	126620 ų
包络体积 envelope_volume	158690 ų
水化壳体积 shell_volume	41953 ų
包络直径 envelope_diameter	109.7 Å
壳层 Rg shell_rg	38.62 Å
包络 Rg envelope_rg	31.74 Å
形状 Rg shape_rg	31.74 Å
总 Rg total_rg	32.16 Å
总原子数 total_atoms	7205
残基数 n_residues	871
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	103.9 Å
Rg (实空间) rg_real	32.56 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	1.7790e+08
I(0) 误差 (实空间) i0_real_error	2.5170e+06
Rg (倒空间) rg_reciprocal	32.62 Å
I(0) (倒空间) i0_reciprocal	177900000.0000
解质量估计 total_estimate	0.9008
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	43.3 Å
偏度 Skewness skewness	0.186
峰度 Kurtosis kurtosis	-0.552
角度范围 angular_range	— – 0.2400 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	76740000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.911

晶胞参数 Unit Cell

晶胞边长 a length_a	56.365 Å
晶胞边长 b length_b	133.269 Å
晶胞边长 c length_c	79.165 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.92 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

对称性 Symmetry

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

精修参数 Refinement

分辨率 resolution	1.880 Å
最低分辨率 resolution_low	37.660 Å
R 因子 r_factor	0.1966
R_work r_work	0.1960
R_free r_free	0.2218

衍射实验 Diffraction

实验温度 temperature

80.0 K

Files (7)

• pr_distribution /app/data/pr_computation/db/9dbh/pr_distribution.json
• pr_output /app/data/pr_computation/db/9dbh/9dbh.pr.out
• pr_plot /app/data/visualization/pr_computation/db/9dbh/9dbh_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/db/9dbh/9dbh.dat
• saxs_fit /app/data/saxs_computation/db/9dbh/9dbh.fit
• saxs_log /app/data/saxs_computation/db/9dbh/9dbh.log
• saxs_plot /app/data/visualization/saxs_computation/db/9dbh/9dbh_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/db/9dbh/9dbh.fit
pddf	/app/data/pr_computation/db/9dbh/9dbh.pr.out
profile	/app/data/saxs_computation/db/9dbh/9dbh.dat