8snp

Crystal structure of mouse Netrin-1 in complex with samarium ions

Method: X-RAY DIFFRACTION D_max: 136.7 Å Quality: REASONABLE

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8snp
沉积日期 deposition_date	2023-04-27
结构标题 title	Crystal structure of mouse Netrin-1 in complex with samarium ions
关键词 keywords	Extracellular matrix protein, apoptosis, axon guidance, neuronal development, cell signaling; APOPTOSIS
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	34.85 Å
回转半径 Rg (电子) rg_electron	35.98 Å
零角强度 I(0) i0	44270100.00
分子量 molecular_weight	46972.0 kDa
排除体积 excluded_volume	56261 Å³
包络体积 envelope_volume	81046 Å³
水化壳体积 shell_volume	22422 Å³
包络直径 envelope_diameter	142.9 Å
壳层 Rg shell_rg	34.17 Å
包络 Rg envelope_rg	38.47 Å
形状 Rg shape_rg	35.93 Å
总 Rg total_rg	36.00 Å
总原子数 total_atoms	6188
残基数 n_residues	409
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	136.7 Å
Rg (实空间) rg_real	35.79 Å
Rg 误差 (实空间) rg_real_error	2.10 Å
I(0) (实空间) i0_real	4.4270e+07
I(0) 误差 (实空间) i0_real_error	7.7370e+05
Rg (倒空间) rg_reciprocal	35.20 Å
I(0) (倒空间) i0_reciprocal	44250000.0000
解质量估计 total_estimate	0.6617
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	24.3 Å
偏度 Skewness skewness	0.841
峰度 Kurtosis kurtosis	0.115
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2244000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.238; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.059; Smooth: 0.823

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Netrin-1
分子量 formula_weight	67922.5 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	6188

MMRAVWEALAALAAVACLVGAVRGGPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNSSDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYYYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKIPVAPPTTAASSVEEPEDCDSYCKASKGKLKMNMKKYCRKDYAVQIHILKADKAGDWWKFTVNIISVYKQGTSRIRRGDQSLWIRSRDIACKCPKIKPLKKYLLLGNAEDSPDQSGIVADKSSLVIQWRDTWARRLRKFQQREKKGKCKKA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	570.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	SAMARIUM (III) ION
分子量 formula_weight	150.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	69.500 Å
晶胞边长 b length_b	69.500 Å
晶胞边长 c length_c	333.641 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	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	trigonal

分辨率 resolution	3.400 Å
最低分辨率 resolution_low	56.620 Å
R 因子 r_factor	0.2505
R_work r_work	0.2496
R_free r_free	0.2683

fit	/app/data/saxs_computation/sn/8snp/8snp.fit
pddf	/app/data/pr_computation/sn/8snp/8snp.pr.out
profile	/app/data/saxs_computation/sn/8snp/8snp.dat

Crystal structure of mouse Netrin-1 in complex with samarium ions

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