9bdj

MicroED structure of bovine liver catalase with missing cone eliminated by suspended drop

Method: ELECTRON CRYSTALLOGRAPHY D_max: 114.5 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	9bdj
沉积日期 deposition_date	2024-04-11
结构标题 title	MicroED structure of bovine liver catalase with missing cone eliminated by suspended drop
关键词 keywords	Heme-containing enzyme, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	ELECTRON CRYSTALLOGRAPHY

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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	37.29 Å
回转半径 Rg (电子) rg_electron	36.47 Å
零角强度 I(0) i0	843489000.00
分子量 molecular_weight	232570.0 kDa
排除体积 excluded_volume	288170 Å³
包络体积 envelope_volume	353120 Å³
水化壳体积 shell_volume	74808 Å³
包络直径 envelope_diameter	118.9 Å
壳层 Rg shell_rg	46.70 Å
包络 Rg envelope_rg	36.48 Å
形状 Rg shape_rg	36.46 Å
总 Rg total_rg	37.06 Å
总原子数 total_atoms	16432
残基数 n_residues	1996
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	114.5 Å
Rg (实空间) rg_real	37.03 Å
Rg 误差 (实空间) rg_real_error	0.52 Å
I(0) (实空间) i0_real	8.4350e+08
I(0) 误差 (实空间) i0_real_error	1.0900e+07
Rg (倒空间) rg_reciprocal	37.19 Å
I(0) (倒空间) i0_reciprocal	843600000.0000
解质量估计 total_estimate	0.8951
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	46.4 Å
偏度 Skewness skewness	0.131
峰度 Kurtosis kurtosis	-0.518
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	326700000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.902

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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	Catalase
分子量 formula_weight	59999.2 kDa
EC 编号 ec_number	1.11.1.6
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	16432

MADNRDPASDQMKHWKEQRAAQKPDVLTTGGGNPVGDKLNSLTVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITRYSKAKVFEHIGKRTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDALLFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLAHEDPDYGLRDLFNAIATGNYPSWTLYIQVMTFSEAEIFPFNPFDLTKVWPHGDYPLIPVGKLVLNRNPVNYFAEVEQLAFDPSNMPPGIEPSPDKMLQGRLFAYPDTHRHRLGPNYLQIPVNCPYRARVANYQRDGPMCMMDNQGGAPNYYPNSFSAPEHQPSALEHRTHFSGDVQRFNSANDDNVTQVRTFYLKVLNEEQRKRLCENIAGHLKDAQLFIQKKAVKNFSDVHPEYGSRIQALLDKYNEEKPKNAVHTYVQHGSHLSAREKANL

Entity 2 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	745.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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7. 引用文献 (1)

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晶胞边长 a length_a	68.650 Å
晶胞边长 b length_b	173.300 Å
晶胞边长 c length_c	182.780 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	4.000 Å
最低分辨率 resolution_low	44.109 Å
R 因子 r_factor	—
R_work r_work	0.3166
R_free r_free	0.3580

分辨率 resolution	4.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	—

fit	/app/data/saxs_computation/bd/9bdj/9bdj.fit
pddf	/app/data/pr_computation/bd/9bdj/9bdj.pr.out
profile	/app/data/saxs_computation/bd/9bdj/9bdj.dat

MicroED structure of bovine liver catalase with missing cone eliminated by suspended drop

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 non-polymer

Entity 3 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)