8g9d
;Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5- phosphonodifluoroacetamide inositol pentakisphosphate (5-PCF2Am-InsP5), an analogue of 5-InsP7 ;
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
| 条目编号 entry_id | 8g9d |
| 沉积日期 deposition_date | 2023-02-21 |
| 最后修订 last_revision | 2024-01-03 |
| 结构标题 title | ;Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5- phosphonodifluoroacetamide inositol pentakisphosphate (5-PCF2Am-InsP5), an analogue of 5-InsP7 ; |
| 关键词 keywords | phosphatase, nudix, catalysis mechanism, Substrate Specificity, inositol, inositol pyrophosphate, HYDROLASE; HYDROLASE |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 15.19 Å |
| 回转半径 Rg (电子) rg_electron | 14.07 Å |
| 零角强度 I(0) i0 | 5892680.00 |
| 分子量 molecular_weight | 16267.0 kDa |
| 排除体积 excluded_volume | 19822 ų |
| 包络体积 envelope_volume | 22280 ų |
| 水化壳体积 shell_volume | 13223 ų |
| 包络直径 envelope_diameter | 47.8 Å |
| 壳层 Rg shell_rg | 20.11 Å |
| 包络 Rg envelope_rg | 14.38 Å |
| 形状 Rg shape_rg | 14.09 Å |
| 总 Rg total_rg | 15.15 Å |
| 总原子数 total_atoms | 1136 |
| 残基数 n_residues | 135 |
| 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 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 47.8 Å |
| Rg (实空间) rg_real | 15.07 Å |
| Rg 误差 (实空间) rg_real_error | 0.19 Å |
| I(0) (实空间) i0_real | 5.8930e+06 |
| I(0) 误差 (实空间) i0_real_error | 5.7680e+04 |
| Rg (倒空间) rg_reciprocal | 15.08 Å |
| I(0) (倒空间) i0_reciprocal | 5893000.0000 |
| 解质量估计 total_estimate | 0.8925 |
| 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 | 19.4 Å |
| 偏度 Skewness skewness | 0.111 |
| 峰度 Kurtosis kurtosis | -0.412 |
| 角度范围 angular_range | — – 0.5000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 1240000.0000 |
| 实空间数据点数 n_real_points | 80 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.969 |