Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant

条目编号 entry_id	8th5
沉积日期 deposition_date	2023-07-13
结构标题 title	Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant
关键词 keywords	NTF2L USP10, PEPTIDE BINDING PROTEIN, Hydrolase-Viral Protein complex; Hydrolase/Viral Protein
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	39.13 Å
回转半径 Rg (电子) rg_electron	38.58 Å
零角强度 I(0) i0	324870000.00
分子量 molecular_weight	144840.0 kDa
排除体积 excluded_volume	180830 ų
包络体积 envelope_volume	273970 ų
水化壳体积 shell_volume	59213 ų
包络直径 envelope_diameter	145.1 Å
壳层 Rg shell_rg	44.76 Å
包络 Rg envelope_rg	37.37 Å
形状 Rg shape_rg	38.55 Å
总 Rg total_rg	39.11 Å
总原子数 total_atoms	10235
残基数 n_residues	1293
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	131.5 Å
Rg (实空间) rg_real	38.88 Å
Rg 误差 (实空间) rg_real_error	0.98 Å
I(0) (实空间) i0_real	3.2490e+08
I(0) 误差 (实空间) i0_real_error	5.2410e+06
Rg (倒空间) rg_reciprocal	39.04 Å
I(0) (倒空间) i0_reciprocal	324900000.0000
解质量估计 total_estimate	0.8648
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	49.3 Å
偏度 Skewness skewness	0.139
峰度 Kurtosis kurtosis	-0.291
角度范围 angular_range	— – 0.2000 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21560000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.989

晶胞参数 Unit Cell

晶胞边长 a length_a	61.600 Å
晶胞边长 b length_b	69.450 Å
晶胞边长 c length_c	101.040 Å
晶胞夹角 α angle_alpha	70.66 °
晶胞夹角 β angle_beta	76.86 °
晶胞夹角 γ angle_gamma	88.31 °
晶胞分子数 Z z_pdb	10

对称性 Symmetry

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

精修参数 Refinement

分辨率 resolution	2.620 Å
最低分辨率 resolution_low	46.700 Å
R 因子 r_factor	0.2310
R_work r_work	0.2257
R_free r_free	0.3362

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/th/8th5/pr_distribution.json
• pr_output /app/data/pr_computation/th/8th5/8th5.pr.out
• pr_plot /app/data/visualization/pr_computation/th/8th5/8th5_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/th/8th5/8th5.dat
• saxs_fit /app/data/saxs_computation/th/8th5/8th5.fit
• saxs_log /app/data/saxs_computation/th/8th5/8th5.log
• saxs_plot /app/data/visualization/saxs_computation/th/8th5/8th5_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/th/8th5/8th5.fit
pddf	/app/data/pr_computation/th/8th5/8th5.pr.out
profile	/app/data/saxs_computation/th/8th5/8th5.dat