SAXSdb — 9ikm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9ikm
沉积日期 deposition_date	2024-06-27
结构标题 title	Cryo-EM structure of TLP-4
关键词 keywords	Fibril, PROTEIN FIBRIL; PROTEIN FIBRIL
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	63.77 Å
回转半径 Rg (电子) rg_electron	66.50 Å
零角强度 I(0) i0	619800000.00
分子量 molecular_weight	133940.0 kDa
排除体积 excluded_volume	128110 Å³
包络体积 envelope_volume	299550 Å³
水化壳体积 shell_volume	47468 Å³
包络直径 envelope_diameter	247.8 Å
壳层 Rg shell_rg	45.46 Å
包络 Rg envelope_rg	67.30 Å
形状 Rg shape_rg	66.49 Å
总 Rg total_rg	65.97 Å
总原子数 total_atoms	9720
残基数 n_residues	54
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	221.7 Å
Rg (实空间) rg_real	65.83 Å
Rg 误差 (实空间) rg_real_error	3.00 Å
I(0) (实空间) i0_real	6.1960e+08
I(0) 误差 (实空间) i0_real_error	1.5520e+07
Rg (倒空间) rg_reciprocal	61.92 Å
I(0) (倒空间) i0_reciprocal	615600000.0000
解质量估计 total_estimate	0.5998
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	35.5 Å
偏度 Skewness skewness	0.678
峰度 Kurtosis kurtosis	-0.411
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0008
最高正则化参数 α highest_alpha	10260000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.148; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.130; Smooth: 0.222

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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	TLP-4
分子量 formula_weight	7008.7 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	A
原子数 atom_count	9720

XTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTASXTAS

Entity 2 branched

描述 description	;alpha-L-arabinofuranose-(1-2)-beta-D-galactopyranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-3)]beta-L-arabinofuranose-(1-3)-alpha-L-arabinofuranose ;
分子量 formula_weight	972.8 kDa
来源方法 src_method	man
拷贝数 entity_count	18

Entity 3 branched

描述 description	;alpha-L-arabinofuranose-(1-3)-alpha-L-arabinofuranose-(1-3)-alpha-D-mannopyranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-4)][alpha-L-arabinofuranose-(1-6)]beta-D-galactopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[alpha-L-arabinofuranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-6)]beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-[alpha-L-arabinofuranose-(1-2)][alpha-L-arabinofuranose-(1-6)]beta-D-mannopyranose-(1-6)][beta-L-arabinofuranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-L-arabinofuranose-(1-3)]2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)]beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose ;
分子量 formula_weight	4280.7 kDa
来源方法 src_method	man
拷贝数 entity_count	18

Entity 4 branched

描述 description	;alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)-alpha-L-arabinofuranose-(1-2)-alpha-D-mannopyranose-(1-2)-[beta-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)-alpha-L-arabinofuranose-(1-3)]alpha-L-arabinofuranose-(1-4)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-L-arabinofuranose-(1-2)]beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-2)]beta-D-mannopyranose-(1-4)-[alpha-L-arabinofuranose-(1-2)]beta-D-galactopyranose ;
分子量 formula_weight	2342.0 kDa
来源方法 src_method	man
拷贝数 entity_count	18

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7. 引用文献 (1)

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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	—

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

分辨率 resolution	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	27189

fit	/app/data/saxs_computation/ik/9ikm/9ikm.fit
pddf	/app/data/pr_computation/ik/9ikm/9ikm.pr.out
profile	/app/data/saxs_computation/ik/9ikm/9ikm.dat

Cryo-EM structure of TLP-4

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 branched

Entity 3 branched

Entity 4 branched

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)