1hb9

quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography.

Method: ELECTRON MICROSCOPY D_max: 194.1 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	1hb9
沉积日期 deposition_date	2001-04-13
结构标题 title	quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography.
关键词 keywords	VIRUS, VIRUS/VIRAL PROTEIN, TECTIVIRIDAE, BACTERIOPHAGE PRD1, CRYO- EM, IMAGE RECONSTRUCTION, ICOSAHEDRAL VIRUS; VIRUS
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	59.29 Å
回转半径 Rg (电子) rg_electron	59.27 Å
零角强度 I(0) i0	3335330000.00
分子量 molecular_weight	486830.0 kDa
排除体积 excluded_volume	608590 Å³
包络体积 envelope_volume	846560 Å³
水化壳体积 shell_volume	118930 Å³
包络直径 envelope_diameter	213.8 Å
壳层 Rg shell_rg	60.74 Å
包络 Rg envelope_rg	58.58 Å
形状 Rg shape_rg	59.27 Å
总 Rg total_rg	59.31 Å
总原子数 total_atoms	34416
残基数 n_residues	4460
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	194.1 Å
Rg (实空间) rg_real	59.48 Å
Rg 误差 (实空间) rg_real_error	1.83 Å
I(0) (实空间) i0_real	3.3350e+09
I(0) 误差 (实空间) i0_real_error	7.1030e+07
Rg (倒空间) rg_reciprocal	59.11 Å
I(0) (倒空间) i0_reciprocal	3333000000.0000
解质量估计 total_estimate	0.8448
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	59.7 Å
偏度 Skewness skewness	0.446
峰度 Kurtosis kurtosis	-0.192
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	853700000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.339

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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 (1)

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1hb9a_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9b_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9c_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9d_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9e_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9f_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9g_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9h_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9i_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9j_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9k_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1hb9l_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

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7. 引用文献 (4)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	25.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	25.00 Å
分辨率测定方法 resolution_method	ICOSAHEDRAL
颗粒数 num_particles	1800

描述 description	BACTERIOPHAGE PRD1
分子量 formula_weight	43346.2 kDa
来源方法 src_method	man
拷贝数 entity_count	12

quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography.

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	36364

来源生物 organism	BACTERIOPHAGE PRD1
NCBI 分类编号 ncbi_taxonomy_id	10658
宿主生物 host_organism	SALMONELLA TYPHIMURIUM

fit	/app/data/saxs_computation/hb/1hb9/1hb9.fit
pddf	/app/data/pr_computation/hb/1hb9/1hb9.pr.out
profile	/app/data/saxs_computation/hb/1hb9/1hb9.dat