A neutralizing nanobody VHH60 against wt SARS-CoV-2

条目编号 entry_id	8xk2
沉积日期 deposition_date	2023-12-22
结构标题 title	A neutralizing nanobody VHH60 against wt SARS-CoV-2
关键词 keywords	;COVID-19, spike glycoprotein, virus, antibody, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex ;; ANTIVIRAL PROTEIN/IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	36.97 Å
回转半径 Rg (电子) rg_electron	36.54 Å
零角强度 I(0) i0	279021000.00
分子量 molecular_weight	133210.0 kDa
排除体积 excluded_volume	165610 ų
包络体积 envelope_volume	225660 ų
水化壳体积 shell_volume	51980 ų
包络直径 envelope_diameter	137.3 Å
壳层 Rg shell_rg	42.35 Å
包络 Rg envelope_rg	36.15 Å
形状 Rg shape_rg	36.48 Å
总 Rg total_rg	37.14 Å
总原子数 total_atoms	18253
残基数 n_residues	1202
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/ų
壳层衬度 contrast_shell	0.0300 e/ų
CRYSOL 版本 crysol_version	4.1.3

最大尺寸 Dmax dmax	128.8 Å
Rg (实空间) rg_real	36.84 Å
Rg 误差 (实空间) rg_real_error	1.18 Å
I(0) (实空间) i0_real	2.7900e+08
I(0) 误差 (实空间) i0_real_error	4.9910e+06
Rg (倒空间) rg_reciprocal	36.93 Å
I(0) (倒空间) i0_reciprocal	279000000.0000
解质量估计 total_estimate	0.8615
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	47.9 Å
偏度 Skewness skewness	0.250
峰度 Kurtosis kurtosis	-0.147
角度范围 angular_range	— – 0.2150 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26320000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.984

晶胞参数 Unit Cell

晶胞边长 a length_a	80.850 Å
晶胞边长 b length_b	100.610 Å
晶胞边长 c length_c	227.430 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

对称性 Symmetry

空间群 space_group	P 2 2 21
空间群编号 int_tables_number	17
晶系 crystal_system	orthorhombic

精修参数 Refinement

分辨率 resolution	3.400 Å
最低分辨率 resolution_low	31.210 Å
R 因子 r_factor	0.2592
R_work r_work	0.2557
R_free r_free	0.3000

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/xk/8xk2/pr_distribution.json
• pr_output /app/data/pr_computation/xk/8xk2/8xk2.pr.out
• pr_plot /app/data/visualization/pr_computation/xk/8xk2/8xk2_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/xk/8xk2/8xk2.dat
• saxs_fit /app/data/saxs_computation/xk/8xk2/8xk2.fit
• saxs_log /app/data/saxs_computation/xk/8xk2/8xk2.log
• saxs_plot /app/data/visualization/saxs_computation/xk/8xk2/8xk2_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/xk/8xk2/8xk2.fit
pddf	/app/data/pr_computation/xk/8xk2/8xk2.pr.out
profile	/app/data/saxs_computation/xk/8xk2/8xk2.dat