8kf1

The cryo-EM structure of AV-45 bound type1 amyloid beta 42 fibril.

Method: ELECTRON MICROSCOPY D_max: 66.3 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	8kf1
沉积日期 deposition_date	2023-08-15
最后修订 last_revision	2024-08-21
结构标题 title	The cryo-EM structure of AV-45 bound type1 amyloid beta 42 fibril.
关键词 keywords	amyloid, 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	22.64 Å
回转半径 Rg (电子) rg_electron	20.76 Å
零角强度 I(0) i0	27612500.00
分子量 molecular_weight	43183.0 kDa
排除体积 excluded_volume	55271 Å³
包络体积 envelope_volume	62665 Å³
水化壳体积 shell_volume	24568 Å³
包络直径 envelope_diameter	67.8 Å
壳层 Rg shell_rg	28.11 Å
包络 Rg envelope_rg	21.08 Å
形状 Rg shape_rg	20.79 Å
总 Rg total_rg	21.61 Å
总原子数 total_atoms	3052
残基数 n_residues	408
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	66.3 Å
Rg (实空间) rg_real	22.50 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	2.7610e+07
I(0) 误差 (实空间) i0_real_error	3.2520e+05
Rg (倒空间) rg_reciprocal	22.54 Å
I(0) (倒空间) i0_reciprocal	27610000.0000
解质量估计 total_estimate	0.8392
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	32.1 Å
偏度 Skewness skewness	0.070
峰度 Kurtosis kurtosis	-0.599
角度范围 angular_range	— – 0.3500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4948000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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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 (2)

Entity 1 polymer

描述 description	P3(40)
分子量 formula_weight	87046.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,F,H,A,I,B,J,C,K,D,L,E
原子数 atom_count	3052

MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEAEEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSAMSQSLLKTTQEPLARDPVKLPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN

Entity 2 non-polymer

描述 description	4-[2-[6-[2-[2-(2-fluoranylethoxy)ethoxy]ethoxy]pyridin-3-yl]ethyl]-~{N}-methyl-aniline
分子量 formula_weight	362.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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7. 引用文献 (1)

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分辨率 resolution	3.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	11034

fit	/app/data/saxs_computation/kf/8kf1/8kf1.fit
pddf	/app/data/pr_computation/kf/8kf1/8kf1.pr.out
profile	/app/data/saxs_computation/kf/8kf1/8kf1.dat