Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE

条目编号 entry_id	8ydv
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 Omicron BA.5 variant spike protein in complex with CeSPIACE
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	30.21 Å
回转半径 Rg (电子) rg_electron	30.25 Å
零角强度 I(0) i0	47149400.00
分子量 molecular_weight	53812.0 kDa
排除体积 excluded_volume	67206 ų
包络体积 envelope_volume	82832 ų
水化壳体积 shell_volume	25427 ų
包络直径 envelope_diameter	115.5 Å
壳层 Rg shell_rg	33.22 Å
包络 Rg envelope_rg	30.77 Å
形状 Rg shape_rg	30.20 Å
总 Rg total_rg	30.72 Å
总原子数 total_atoms	3791
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	109.7 Å
Rg (实空间) rg_real	30.69 Å
Rg 误差 (实空间) rg_real_error	1.17 Å
I(0) (实空间) i0_real	4.7150e+07
I(0) 误差 (实空间) i0_real_error	7.7190e+05
Rg (倒空间) rg_reciprocal	30.48 Å
I(0) (倒空间) i0_reciprocal	47140000.0000
解质量估计 total_estimate	0.7308
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	25.3 Å
偏度 Skewness skewness	0.703
峰度 Kurtosis kurtosis	0.038
角度范围 angular_range	— – 0.2600 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11010000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.556; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.393; Smooth: 0.438

晶胞参数 Unit Cell

晶胞边长 a length_a	87.480 Å
晶胞边长 b length_b	87.480 Å
晶胞边长 c length_c	118.230 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	8

对称性 Symmetry

空间群 space_group	P 41
空间群编号 int_tables_number	76
晶系 crystal_system	tetragonal

精修参数 Refinement

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	48.980 Å
R 因子 r_factor	0.1966
R_work r_work	0.1953
R_free r_free	0.2210

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

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

Curves (3)

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