8qvf

Comparison of room-temperature and cryogenic structures of soluble Epoxide Hydrolase with ligands bound.

Method: X-RAY DIFFRACTION D_max: 98.8 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	8qvf
沉积日期 deposition_date	2023-10-18
结构标题 title	Comparison of room-temperature and cryogenic structures of soluble Epoxide Hydrolase with ligands bound.
关键词 keywords	Inhibitor, serial crystallography, drug discovery, fixed target, room temperature, microcrystals, HYDROLASE; HYDROLASE
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	29.47 Å
回转半径 Rg (电子) rg_electron	28.97 Å
零角强度 I(0) i0	59854700.00
分子量 molecular_weight	61768.0 kDa
排除体积 excluded_volume	77830 Å³
包络体积 envelope_volume	96448 Å³
水化壳体积 shell_volume	28862 Å³
包络直径 envelope_diameter	104.0 Å
壳层 Rg shell_rg	34.76 Å
包络 Rg envelope_rg	28.94 Å
形状 Rg shape_rg	28.95 Å
总 Rg total_rg	29.64 Å
总原子数 total_atoms	4333
残基数 n_residues	546
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	98.8 Å
Rg (实空间) rg_real	29.62 Å
Rg 误差 (实空间) rg_real_error	0.97 Å
I(0) (实空间) i0_real	5.9850e+07
I(0) 误差 (实空间) i0_real_error	9.3790e+05
Rg (倒空间) rg_reciprocal	29.56 Å
I(0) (倒空间) i0_reciprocal	59850000.0000
解质量估计 total_estimate	0.8497
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	27.4 Å
偏度 Skewness skewness	0.451
峰度 Kurtosis kurtosis	-0.480
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19890000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.836

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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	Bifunctional epoxide hydrolase 2
分子量 formula_weight	62002.7 kDa
来源方法 src_method	man
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	4459

GMTLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera

Entity 2 non-polymer

描述 description	1-(1-adamantyl)-3-(1-methylsulfonylpiperidin-4-yl)urea
分子量 formula_weight	355.5 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	98

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7. 引用文献 (1)

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晶胞边长 a length_a	95.410 Å
晶胞边长 b length_b	95.410 Å
晶胞边长 c length_c	244.290 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	44.440 Å
R 因子 r_factor	0.1877
R_work r_work	0.1858
R_free r_free	0.2228

fit	/app/data/saxs_computation/qv/8qvf/8qvf.fit
pddf	/app/data/pr_computation/qv/8qvf/8qvf.pr.out
profile	/app/data/saxs_computation/qv/8qvf/8qvf.dat

Comparison of room-temperature and cryogenic structures of soluble Epoxide Hydrolase with ligands bound.

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