9is7

Paracandidimonas lactea CP group II intron 2S state

Method: ELECTRON MICROSCOPY D_max: 149.4 Å Quality: REASONABLE

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	9is7
沉积日期 deposition_date	2024-07-17
结构标题 title	Paracandidimonas lactea CP group II intron 2S state
关键词 keywords	CryoEM, Ribozyme, RNA; RNA
实验方法 method	ELECTRON MICROSCOPY

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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	44.98 Å
回转半径 Rg (电子) rg_electron	44.71 Å
零角强度 I(0) i0	2405380000.00
分子量 molecular_weight	230860.0 kDa
排除体积 excluded_volume	214700 Å³
包络体积 envelope_volume	422100 Å³
水化壳体积 shell_volume	78754 Å³
包络直径 envelope_diameter	160.8 Å
壳层 Rg shell_rg	49.62 Å
包络 Rg envelope_rg	43.58 Å
形状 Rg shape_rg	44.69 Å
总 Rg total_rg	44.88 Å
总原子数 total_atoms	15216
残基数 n_residues	705
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	149.4 Å
Rg (实空间) rg_real	44.86 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	2.4050e+09
I(0) 误差 (实空间) i0_real_error	4.8440e+07
Rg (倒空间) rg_reciprocal	44.98 Å
I(0) (倒空间) i0_reciprocal	2406000000.0000
解质量估计 total_estimate	0.6455
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	51.2 Å
偏度 Skewness skewness	0.312
峰度 Kurtosis kurtosis	-0.229
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	152600000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.995; Smooth: 0.900

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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	RNA (153-MER)
分子量 formula_weight	49428.5 kDa
来源方法 src_method	man
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	15216

AGCAGGCGCCACCUGCUGCGGAACCGCUGAAGCCGCGUGCCUCUAACAGGGCUGGCGCGGCUACGAAGGGCGCUGGGGGUGGGAACCACCUCCUUCGACCCAAUCCAUGGCCUGCGCCGCAACGUGCAGGCCAGCAGUCUCCACGACAAGGAG

来源 Source

来源生物 organism	Paracandidimonas lactea
NCBI 分类编号 ncbi_taxonomy_id	2895524
宿主生物 host_organism	synthetic construct

Entity 2 polymer

描述 description	RNA (582-MER)
分子量 formula_weight	189407.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

GGGCGACUACGAAACGGGCCUGGGUAGGAAAUGACCCAGUGACCCUGACAGUUUGGGAAAGUCGGUGAAAGCCCGACCCUCGGGGCCUAGCGAAAGUGGGCGACGAGUGCAACACCUGGAGGCUGAGGGCGUCAGUGAUGGCGUCAGGCAUGCGGGAGAAAUCUAGGCAUGCUGGCACCUAUCGAAAGAUGGGGCCGCUGGAUAGCUCAAUCAGGUAAAGGCACCGUUCAGGUGCUGUGUUGAGGCAUAGGAAGGCAGGGCCGCAGUCGCGGUAAGCAAGCAGCGUUGAAGCGCAUCGGCAGUACCGCAUCCGUUAUGGAACCUUGGGAGCGAGAAACCCUGGAAACGGGGGUAGGGUCAGAGACCUAGAUAAAUCCGAUGUGGCCGAGCUGGCUGUCGUUCGAUGCCGUAGUACUGACUGUCUAAGUAGGGAAGGUCUCGGCAGAUCGUGGGGGUGGCACCCUGCGAAAUUAUCUGCCAAGACUGGGAGAUGGCUUGAGUAGUGCCGCCGCGCGAGCGGUGGGCAGACCAUGGGGGCAGACUUGCUGGAUGUUCCUAUCGGCGAAAGAGCCAAGCGGUAAC

来源 Source

来源生物 organism	Paracandidimonas lactea
NCBI 分类编号 ncbi_taxonomy_id	2895524
宿主生物 host_organism	synthetic construct

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	29

Entity 4 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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7. 引用文献 (1)

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分辨率 resolution	2.87 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	33739

fit	/app/data/saxs_computation/is/9is7/9is7.fit
pddf	/app/data/pr_computation/is/9is7/9is7.pr.out
profile	/app/data/saxs_computation/is/9is7/9is7.dat

Paracandidimonas lactea CP group II intron 2S state

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)