Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41

条目编号 entry_id	8ydt
沉积日期 deposition_date	2024-02-21
结构标题 title	Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41
关键词 keywords	RBD, VIRAL PROTEIN-INHIBITOR COMPLEX; VIRAL PROTEIN/INHIBITOR
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	29.95 Å
回转半径 Rg (电子) rg_electron	29.89 Å
零角强度 I(0) i0	47022500.00
分子量 molecular_weight	53933.0 kDa
排除体积 excluded_volume	67379 ų
包络体积 envelope_volume	83641 ų
水化壳体积 shell_volume	25640 ų
包络直径 envelope_diameter	113.0 Å
壳层 Rg shell_rg	33.37 Å
包络 Rg envelope_rg	30.57 Å
形状 Rg shape_rg	29.81 Å
总 Rg total_rg	30.48 Å
总原子数 total_atoms	3806
残基数 n_residues	470
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	107.8 Å
Rg (实空间) rg_real	30.37 Å
Rg 误差 (实空间) rg_real_error	1.34 Å
I(0) (实空间) i0_real	4.7020e+07
I(0) 误差 (实空间) i0_real_error	8.2860e+05
Rg (倒空间) rg_reciprocal	30.19 Å
I(0) (倒空间) i0_reciprocal	47020000.0000
解质量估计 total_estimate	0.7733
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	24.4 Å
偏度 Skewness skewness	0.668
峰度 Kurtosis kurtosis	-0.027
角度范围 angular_range	— – 0.2650 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12010000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.590; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.772

晶胞参数 Unit Cell

晶胞边长 a length_a	73.307 Å
晶胞边长 b length_b	73.307 Å
晶胞边长 c length_c	99.799 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

对称性 Symmetry

空间群 space_group	P 31
空间群编号 int_tables_number	144
晶系 crystal_system	trigonal

精修参数 Refinement

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	39.230 Å
R 因子 r_factor	0.2306
R_work r_work	0.2286
R_free r_free	0.2680

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/yd/8ydt/pr_distribution.json
• pr_output /app/data/pr_computation/yd/8ydt/8ydt.pr.out
• pr_plot /app/data/visualization/pr_computation/yd/8ydt/8ydt_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/yd/8ydt/8ydt.dat
• saxs_fit /app/data/saxs_computation/yd/8ydt/8ydt.fit
• saxs_log /app/data/saxs_computation/yd/8ydt/8ydt.log
• saxs_plot /app/data/visualization/saxs_computation/yd/8ydt/8ydt_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/yd/8ydt/8ydt.fit
pddf	/app/data/pr_computation/yd/8ydt/8ydt.pr.out
profile	/app/data/saxs_computation/yd/8ydt/8ydt.dat