9hu4

Asymmetric unit from transcribing double-layered particle of bacteriophage phi6

Method: ELECTRON MICROSCOPY D_max: 193.9 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	9hu4
沉积日期 deposition_date	2024-12-20
结构标题 title	Asymmetric unit from transcribing double-layered particle of bacteriophage phi6
关键词 keywords	;cystovirus, phi6, semi-conservative transcription, cryo-EM, cryogenic electron microscopy, localized reconstruction, symmetry relaxation, virus, dsRNA virus, bacteriophage ;; 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	57.19 Å
回转半径 Rg (电子) rg_electron	57.71 Å
零角强度 I(0) i0	1552660000.00
分子量 molecular_weight	332630.0 kDa
排除体积 excluded_volume	418390 Å³
包络体积 envelope_volume	664390 Å³
水化壳体积 shell_volume	99565 Å³
包络直径 envelope_diameter	210.1 Å
壳层 Rg shell_rg	56.22 Å
包络 Rg envelope_rg	57.44 Å
形状 Rg shape_rg	57.71 Å
总 Rg total_rg	57.69 Å
总原子数 total_atoms	23399
残基数 n_residues	3051
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	193.9 Å
Rg (实空间) rg_real	57.57 Å
Rg 误差 (实空间) rg_real_error	1.99 Å
I(0) (实空间) i0_real	1.5530e+09
I(0) 误差 (实空间) i0_real_error	3.4620e+07
Rg (倒空间) rg_reciprocal	56.85 Å
I(0) (倒空间) i0_reciprocal	1551000000.0000
解质量估计 total_estimate	0.8330
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	57.4 Å
偏度 Skewness skewness	0.577
峰度 Kurtosis kurtosis	-0.060
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	303300000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.459

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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 (3)

Entity 1 polymer

描述 description	Major inner protein P1
分子量 formula_weight	84783.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	23399

MFNLKVKDLNGSARGLTQAFAIGELKNQLSVGALQLPLQFTRTFSASMTSELLWEVGKGNIDPVMYARLFFQYAQAGGALSVDELVNQFTEYHQSTACNPEIWRKLTAYITGSSNRAIKADAVGKVPPTAILEQLRTLAPSEHELFHHITTDFVCHVLSPLGFILPDAAYVYRVGRTATYPNFYALVDCVRASDLRRMLTALSSVDSKMLQATFKAKGALAPALISQHLANAATTAFERSRGNFDANAVVSSVLTILGRLWSPSTPKELDPSARLRNTNGIDQLRSNLALFIAYQDMVKQRGRAEVIFSDEELSSTIIPWFIEAMSEVSPFKLRPINETTSYIGQTSAIDHMGQPSHVVVYEDWQFAKEITAFTPVKLANNSNQRFLDVEPGISDRMSATLAPIGNTFAVSAFVKNRTAVYEAVSQRGTVNSNGAEMTLGFPSVVERDYALDRDPMVAIAALRTGIVDESLEARASNDLKRSMFNYYAAVMHYAVAHNPEVVVSEHQGVAAEQGSLYLVWNVRTELRIPVGYNAIEGGSIRTPEPLEAIAYNKPIQPSEVLQAKVLDLANHTTSIHIWPWHEASTEFAYEDAYSVTIRNKRYTAEVKEFELLGLGQRRERVRILKPTVAHAIIQMWYSWFVEDDRTLAAARRTSRDDAEKLAIDGRRMQNAVTLLRKIEMIGTTGIGASAVHLAQSRIVDQMAGRGLIDDSSDLHVGINRHRIRIWAGLAVLQMMGLLSRSEAEALTKVLGDSNALGMVVATTDID

Entity 2 polymer

描述 description	NTPase
分子量 formula_weight	4134.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

PTSMKALDHTSIASVAPLERGSVDTDDRNSAPRRGANFS

Entity 3 polymer

描述 description	Major outer capsid protein
分子量 formula_weight	15931.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E,F,G,H,I,J,K,L,M

MLLPVVARAAVPAIESAIAATPGLVSRIAAAIGSKVSPSAILAAVKSNPVVAGLTLAQIGSTGYDAYQQLLENHPEVAEMLKDLSFKADEIQPDFIGNLGQYREELELVEDAARFVGGMSNLIRLRQALELDIKYYGLKMQLNDMGYR

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7. 引用文献 (1)

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分辨率 resolution	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	2504986

fit	/app/data/saxs_computation/hu/9hu4/9hu4.fit
pddf	/app/data/pr_computation/hu/9hu4/9hu4.pr.out
profile	/app/data/saxs_computation/hu/9hu4/9hu4.dat

Asymmetric unit from transcribing double-layered particle of bacteriophage phi6

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)