9kyg
Crystal structure of E.coli ac4C amidohydrolase YqfB in complex with cytidine
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 | 9kyg |
| 沉积日期 deposition_date | 2024-12-09 |
| 结构标题 title | Crystal structure of E.coli ac4C amidohydrolase YqfB in complex with cytidine |
| 关键词 keywords | N4-acetylcytidine, RNA modification, amidohydrolase, cytidine, complex, 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 | 20.65 Å |
| 回转半径 Rg (电子) rg_electron | 20.16 Å |
| 零角强度 I(0) i0 | 10140900.00 |
| 分子量 molecular_weight | 23827.0 kDa |
| 排除体积 excluded_volume | 29747 ų |
| 包络体积 envelope_volume | 35143 ų |
| 水化壳体积 shell_volume | 15305 ų |
| 包络直径 envelope_diameter | 66.0 Å |
| 壳层 Rg shell_rg | 25.07 Å |
| 包络 Rg envelope_rg | 20.01 Å |
| 形状 Rg shape_rg | 20.12 Å |
| 总 Rg total_rg | 20.99 Å |
| 总原子数 total_atoms | 1679 |
| 残基数 n_residues | 203 |
| 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 | 66.6 Å |
| Rg (实空间) rg_real | 20.69 Å |
| Rg 误差 (实空间) rg_real_error | 0.51 Å |
| I(0) (实空间) i0_real | 1.0140e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.3010e+05 |
| Rg (倒空间) rg_reciprocal | 20.68 Å |
| I(0) (倒空间) i0_reciprocal | 10140000.0000 |
| 解质量估计 total_estimate | 0.8046 |
| 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 | 20.3 Å |
| 偏度 Skewness skewness | 0.323 |
| 峰度 Kurtosis kurtosis | -0.636 |
| 角度范围 angular_range | — – 0.3850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2898000.0000 |
| 实空间数据点数 n_real_points | 70 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.841; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.000 |