9fgu

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)

Method: ELECTRON MICROSCOPY D_max: 85.8 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	9fgu
沉积日期 deposition_date	2024-05-25
结构标题 title	SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)
关键词 keywords	SARS-CoV-2, Spike, single chain fragment, VIRAL PROTEIN; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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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	25.23 Å
回转半径 Rg (电子) rg_electron	24.57 Å
零角强度 I(0) i0	35145200.00
分子量 molecular_weight	45880.0 kDa
排除体积 excluded_volume	57461 Å³
包络体积 envelope_volume	72269 Å³
水化壳体积 shell_volume	25449 Å³
包络直径 envelope_diameter	90.1 Å
壳层 Rg shell_rg	30.78 Å
包络 Rg envelope_rg	24.79 Å
形状 Rg shape_rg	24.51 Å
总 Rg total_rg	25.53 Å
总原子数 total_atoms	3241
残基数 n_residues	413
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	85.8 Å
Rg (实空间) rg_real	25.28 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	3.5150e+07
I(0) 误差 (实空间) i0_real_error	5.5590e+05
Rg (倒空间) rg_reciprocal	25.27 Å
I(0) (倒空间) i0_reciprocal	35140000.0000
解质量估计 total_estimate	0.8688
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	29.9 Å
偏度 Skewness skewness	0.451
峰度 Kurtosis kurtosis	-0.167
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11030000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.977

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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	Spike glycoprotein,Fibritin
分子量 formula_weight	135255.2 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	C
原子数 atom_count	3241

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKSKRSFIEDLLFNKVTKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Enterobacteria phage T4
通用名 common_name	Bacteriophage T4
NCBI 分类编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	scFv76-77 single chain fragment
分子量 formula_weight	28197.2 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	E

RTMEEVQLLQSAGGLVQPGGSLRLSCAASGFTVSANYMSWVRQAPGKGLEWVSVIYPGGSTFYADSVKGRFTISKDNSKNTLYLQMNSLRVEDTAVYYCARDLSVAGAFDIWGQGTLVTVSSGGGGSGGGGSGGGGSEIVLTQSPGTLSLSPGEKATLFCRASQTFSSNYLAWYQQKPGQAPSLLIYGGSTRAAGIPDRFSGSGSGTDFTLTINRLEPEDFAIYYCQEYGSSPRVTFGQGTRLEIKRAAAGDYKDDDDKHHHHHH

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 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	1

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

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

分辨率 resolution	4.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	92988

fit	/app/data/saxs_computation/fg/9fgu/9fgu.fit
pddf	/app/data/pr_computation/fg/9fgu/9fgu.pr.out
profile	/app/data/saxs_computation/fg/9fgu/9fgu.dat

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)