2bk2
The prepore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map
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 | 2bk2 |
| 沉积日期 deposition_date | 2005-02-10 |
| 结构标题 title | The prepore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map |
| 关键词 keywords | CYTOLYSIS, HEMOLYSIS, THIOL-ACTIVATED CYTOLYSIN, TOXIN, CRYOEM, CYTOLYTIC PROTEIN; TOXIN |
| 实验方法 method | ELECTRON MICROSCOPY |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 31.87 Å |
| 回转半径 Rg (电子) rg_electron | 32.35 Å |
| 零角强度 I(0) i0 | 40379800.00 |
| 分子量 molecular_weight | 50935.0 kDa |
| 排除体积 excluded_volume | 61886 ų |
| 包络体积 envelope_volume | 51479 ų |
| 水化壳体积 shell_volume | 16473 ų |
| 包络直径 envelope_diameter | 112.5 Å |
| 壳层 Rg shell_rg | 31.55 Å |
| 包络 Rg envelope_rg | 31.33 Å |
| 形状 Rg shape_rg | 32.25 Å |
| 总 Rg total_rg | 32.29 Å |
| 总原子数 total_atoms | — |
| 残基数 n_residues | — |
| 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 | 105.9 Å |
| Rg (实空间) rg_real | 32.48 Å |
| Rg 误差 (实空间) rg_real_error | 0.81 Å |
| I(0) (实空间) i0_real | 4.0380e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.8510e+05 |
| Rg (倒空间) rg_reciprocal | 32.23 Å |
| I(0) (倒空间) i0_reciprocal | 40370000.0000 |
| 解质量估计 total_estimate | 0.7677 |
| 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 | 25.4 Å |
| 偏度 Skewness skewness | 0.635 |
| 峰度 Kurtosis kurtosis | -0.293 |
| 角度范围 angular_range | — – 0.2500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 3717000.0000 |
| 实空间数据点数 n_real_points | 51 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.718; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.548; Smooth: 0.276 |