SAXSdb — 9k2y

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9k2y
沉积日期 deposition_date	2024-10-18
结构标题 title	Human IgG1 Fc fragments, mutant (2CT1.1)
关键词 keywords	antibody, IgG1, IMMUNE SYSTEM; IMMUNE SYSTEM
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	36.10 Å
回转半径 Rg (电子) rg_electron	35.50 Å
零角强度 I(0) i0	157163000.00
分子量 molecular_weight	100850.0 kDa
排除体积 excluded_volume	126350 Å³
包络体积 envelope_volume	177360 Å³
水化壳体积 shell_volume	43369 Å³
包络直径 envelope_diameter	120.3 Å
壳层 Rg shell_rg	40.43 Å
包络 Rg envelope_rg	34.45 Å
形状 Rg shape_rg	35.54 Å
总 Rg total_rg	35.75 Å
总原子数 total_atoms	7106
残基数 n_residues	824
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	119.2 Å
Rg (实空间) rg_real	36.16 Å
Rg 误差 (实空间) rg_real_error	1.22 Å
I(0) (实空间) i0_real	1.5720e+08
I(0) 误差 (实空间) i0_real_error	2.6890e+06
Rg (倒空间) rg_reciprocal	36.13 Å
I(0) (倒空间) i0_reciprocal	157200000.0000
解质量估计 total_estimate	0.8781
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.4 Å
偏度 Skewness skewness	0.366
峰度 Kurtosis kurtosis	-0.427
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13140000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.894

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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 (6)

Entity 1 polymer

描述 description	Immunoglobulin gamma-1 heavy chain
分子量 formula_weight	25244.5 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,A,B,D
原子数 atom_count	7106

TCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSWDERTKEEVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVEASRWWQGNVFSCSVMHEALHNHYTQKSLSRSPGK

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	Homo sapiens

Entity 2 branched

描述 description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1787.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1479.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	951.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose
分子量 formula_weight	383.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	beta-D-galactopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	62.946 Å
晶胞边长 b length_b	123.325 Å
晶胞边长 c length_c	150.026 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	3.120 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2380
R_work r_work	0.2357
R_free r_free	0.2815

fit	/app/data/saxs_computation/k2/9k2y/9k2y.fit
pddf	/app/data/pr_computation/k2/9k2y/9k2y.pr.out
profile	/app/data/saxs_computation/k2/9k2y/9k2y.dat

Human IgG1 Fc fragments, mutant (2CT1.1)

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