8qai

;X-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 7 inner helices, sc-CC-7-LI ;

Method: X-RAY DIFFRACTION D_max: 87.9 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	8qai
沉积日期 deposition_date	2023-08-22
结构标题 title	;X-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 7 inner helices, sc-CC-7-LI ;
关键词 keywords	coiled coil, alpha-helical barrel, de novo protein design, DE NOVO PROTEIN; DE NOVO PROTEIN
实验方法 method	X-RAY DIFFRACTION

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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	28.12 Å
回转半径 Rg (电子) rg_electron	26.91 Å
零角强度 I(0) i0	62284500.00
分子量 molecular_weight	68310.0 kDa
排除体积 excluded_volume	88603 Å³
包络体积 envelope_volume	106290 Å³
水化壳体积 shell_volume	33097 Å³
包络直径 envelope_diameter	88.4 Å
壳层 Rg shell_rg	34.37 Å
包络 Rg envelope_rg	26.65 Å
形状 Rg shape_rg	26.92 Å
总 Rg total_rg	27.72 Å
总原子数 total_atoms	4834
残基数 n_residues	728
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	87.9 Å
Rg (实空间) rg_real	28.09 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	6.2280e+07
I(0) 误差 (实空间) i0_real_error	7.7620e+05
Rg (倒空间) rg_reciprocal	28.11 Å
I(0) (倒空间) i0_reciprocal	62290000.0000
解质量估计 total_estimate	0.8897
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	31.4 Å
偏度 Skewness skewness	0.323
峰度 Kurtosis kurtosis	-0.472
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15050000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.907

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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	sc-CC-7-LI
分子量 formula_weight	39430.7 kDa
来源方法 src_method	man
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	4857

GSHMLIAEALELIAEALFAIALALLAIAKKDKELAKKAVELAEKVYKEAEELYKKAKKKGDLIAAALALIAQALAAIALALAAIALKDKELAKKAYKLAEEVYKKAEKLYEEAKKKGDLIAAALALIAQALALIALALAAIALGDKEKLKEVIEKAKEVYKKAEELYKEAEKKGDLIAAALALIAQALALIAIALAAIALGDEETLKEVKEKAKEVYEKAKKVAEEAEKKGDLIAAALALIAQALALIAIALAAIALGDEEELKKVIEEAKKVYEEAKKIYEEAKKKGDLIAAALALIAQALALIAIALAAIALGDEETLEEARKEAEEVKKEAEELAKEAEQKGNEIAAALAEIAIALAEIAIALVEIAKK

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	23

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7. 引用文献 (1)

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晶胞边长 a length_a	48.207 Å
晶胞边长 b length_b	54.025 Å
晶胞边长 c length_c	74.930 Å
晶胞夹角 α angle_alpha	99.40 °
晶胞夹角 β angle_beta	100.94 °
晶胞夹角 γ angle_gamma	105.33 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	30.630 Å
R 因子 r_factor	0.2015
R_work r_work	0.1990
R_free r_free	0.2368

fit	/app/data/saxs_computation/qa/8qai/8qai.fit
pddf	/app/data/pr_computation/qa/8qai/8qai.pr.out
profile	/app/data/saxs_computation/qa/8qai/8qai.dat

;X-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 7 inner helices, sc-CC-7-LI ;

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

衍射实验 Diffraction