8z79
;Crystal structure of 5-N-alpha-glycinylthymidine (N-alpha-GlyT) FAD-dependent lyase gp47/NGTO from Pseudomonas phage PaMx11 in complex with dsDNA ;
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 | 8z79 |
| 沉积日期 deposition_date | 2024-04-19 |
| 结构标题 title | ;Crystal structure of 5-N-alpha-glycinylthymidine (N-alpha-GlyT) FAD-dependent lyase gp47/NGTO from Pseudomonas phage PaMx11 in complex with dsDNA ; |
| 关键词 keywords | N-alpha-GlyT, hypermodification, DNA, complex, Pseudomonads phage, NGTO, FAD, OXIDOREDUCTASE/DNA, OXIDOREDUCTASE-DNA complex; OXIDOREDUCTASE/DNA |
| 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 | 36.21 Å |
| 回转半径 Rg (电子) rg_electron | 34.84 Å |
| 零角强度 I(0) i0 | 326735000.00 |
| 分子量 molecular_weight | 135940.0 kDa |
| 排除体积 excluded_volume | 165890 ų |
| 包络体积 envelope_volume | 227610 ų |
| 水化壳体积 shell_volume | 53007 ų |
| 包络直径 envelope_diameter | 128.7 Å |
| 壳层 Rg shell_rg | 42.79 Å |
| 包络 Rg envelope_rg | 34.14 Å |
| 形状 Rg shape_rg | 34.81 Å |
| 总 Rg total_rg | 35.48 Å |
| 总原子数 total_atoms | 9527 |
| 残基数 n_residues | 1186 |
| 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 | 118.5 Å |
| Rg (实空间) rg_real | 36.01 Å |
| Rg 误差 (实空间) rg_real_error | 0.71 Å |
| I(0) (实空间) i0_real | 3.2670e+08 |
| I(0) 误差 (实空间) i0_real_error | 5.1550e+06 |
| Rg (倒空间) rg_reciprocal | 36.13 Å |
| I(0) (倒空间) i0_reciprocal | 326800000.0000 |
| 解质量估计 total_estimate | 0.8868 |
| 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 | 48.5 Å |
| 偏度 Skewness skewness | 0.108 |
| 峰度 Kurtosis kurtosis | -0.427 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 40640000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.985 |