8om0

Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B

Method: X-RAY DIFFRACTION D_max: 118.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8om0
沉积日期 deposition_date	2023-03-31
结构标题 title	Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B
关键词 keywords	RIBOZYME, METALLOENZYME, SELF-SPLICING, RETROTRANSPOSITION, RNA; RNA
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	36.47 Å
回转半径 Rg (电子) rg_electron	36.25 Å
零角强度 I(0) i0	739571000.00
分子量 molecular_weight	127020.0 kDa
排除体积 excluded_volume	118310 Å³
包络体积 envelope_volume	200480 Å³
水化壳体积 shell_volume	47206 Å³
包络直径 envelope_diameter	118.7 Å
壳层 Rg shell_rg	41.39 Å
包络 Rg envelope_rg	35.69 Å
形状 Rg shape_rg	36.20 Å
总 Rg total_rg	36.52 Å
总原子数 total_atoms	8375
残基数 n_residues	390
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/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	118.5 Å
Rg (实空间) rg_real	36.42 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	7.3960e+08
I(0) 误差 (实空间) i0_real_error	1.2200e+07
Rg (倒空间) rg_reciprocal	36.46 Å
I(0) (倒空间) i0_reciprocal	739600000.0000
解质量估计 total_estimate	0.8938
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	44.1 Å
偏度 Skewness skewness	0.275
峰度 Kurtosis kurtosis	-0.461
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	27560000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.867

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Domains 1-5
分子量 formula_weight	127991.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A
原子数 atom_count	8375

GGGGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCGCCGUAUACCGAACGGUACGUACGGUGGUGUGG

Entity 2 non-polymer

描述 description	3,4,5-trihydroxybenzoic acid
分子量 formula_weight	170.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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7. 引用文献 (1)

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晶胞边长 a length_a	88.813 Å
晶胞边长 b length_b	94.282 Å
晶胞边长 c length_c	223.875 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.610 Å
最低分辨率 resolution_low	47.350 Å
R 因子 r_factor	0.2407
R_work r_work	0.2379
R_free r_free	0.2960

fit	/app/data/saxs_computation/om/8om0/8om0.fit
pddf	/app/data/pr_computation/om/8om0/8om0.pr.out
profile	/app/data/saxs_computation/om/8om0/8om0.dat

Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction