1ykq
Crystal structure of Diels-Alder ribozyme
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 | 1ykq |
| 沉积日期 deposition_date | 2005-01-18 |
| 结构标题 title | Crystal structure of Diels-Alder ribozyme |
| 关键词 keywords | carbon-carbon bond, catalytic mechanism, RNA crystal structure, Diels-Alder reaction, ribozyme, RNA; RNA |
| 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 | 22.63 Å |
| 回转半径 Rg (电子) rg_electron | 22.36 Å |
| 零角强度 I(0) i0 | 51578900.00 |
| 分子量 molecular_weight | 32172.0 kDa |
| 排除体积 excluded_volume | 29787 ų |
| 包络体积 envelope_volume | 45759 ų |
| 水化壳体积 shell_volume | 18804 ų |
| 包络直径 envelope_diameter | 80.4 Å |
| 壳层 Rg shell_rg | 26.85 Å |
| 包络 Rg envelope_rg | 22.19 Å |
| 形状 Rg shape_rg | 22.29 Å |
| 总 Rg total_rg | 22.82 Å |
| 总原子数 total_atoms | 2090 |
| 残基数 n_residues | 98 |
| 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 | 76.2 Å |
| Rg (实空间) rg_real | 23.45 Å |
| Rg 误差 (实空间) rg_real_error | 0.21 Å |
| I(0) (实空间) i0_real | 5.1480e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.5370e+05 |
| Rg (倒空间) rg_reciprocal | 22.63 Å |
| I(0) (倒空间) i0_reciprocal | 51580000.0000 |
| 解质量估计 total_estimate | 0.6761 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 26.5 Å |
| 偏度 Skewness skewness | 0.408 |
| 峰度 Kurtosis kurtosis | -0.262 |
| 角度范围 angular_range | — – 0.3500 Å−1 |
| 当前正则化参数 α current_alpha | 5.4250 |
| 最高正则化参数 α highest_alpha | 2239000.0000 |
| 实空间数据点数 n_real_points | 67 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.918; Stabil: 0.892; Sysdev: 0.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.457 |