SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
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| 条目编号 entry_id | 9nxz |
| 沉积日期 deposition_date | 2025-03-26 |
| 结构标题 title | Cryo-EM of Class-1 of YM1P nanotube |
| 关键词 keywords | D-peptide, peptide-fiber, helical, PROTEIN FIBRIL; PROTEIN FIBRIL |
| 实验方法 method | ELECTRON MICROSCOPY |
| 回转半径 Rg (Guinier) rg_guinier | 10.26 Å |
| 回转半径 Rg (电子) rg_electron | 8.80 Å |
| 零角强度 I(0) i0 | 105249.00 |
| 分子量 molecular_weight | 1411.0 kDa |
| 排除体积 excluded_volume | 1484 ų |
| 包络体积 envelope_volume | 2367 ų |
| 水化壳体积 shell_volume | 2929 ų |
| 包络直径 envelope_diameter | 29.2 Å |
| 壳层 Rg shell_rg | 12.11 Å |
| 包络 Rg envelope_rg | 9.05 Å |
| 形状 Rg shape_rg | 8.67 Å |
| 总 Rg total_rg | 10.27 Å |
| 总原子数 total_atoms | 106 |
| 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 |
| 最大尺寸 Dmax dmax | 33.4 Å |
| Rg (实空间) rg_real | 10.29 Å |
| Rg 误差 (实空间) rg_real_error | 0.42 Å |
| I(0) (实空间) i0_real | 1.0520e+05 |
| I(0) 误差 (实空间) i0_real_error | 1.3670e+03 |
| Rg (倒空间) rg_reciprocal | 10.29 Å |
| I(0) (倒空间) i0_reciprocal | 105200.0000 |
| 解质量估计 total_estimate | 0.8874 |
| 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 | 11.0 Å |
| 偏度 Skewness skewness | 0.180 |
| 峰度 Kurtosis kurtosis | -0.572 |
| 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 | 6908.0000 |
| 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: 0.901;
Stabil: 0.998;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.905;
Smooth: 0.931
|
冷冻电镜 EM 3D
| 分辨率 resolution | 2.80 Å |
| 分辨率测定方法 resolution_method | — |
| 颗粒数 num_particles | 945036 |
Entity 1
polymer
| 描述 description | YM1P |
| 分子量 formula_weight | 745.7 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(D) |
| 链编号 strand_id | A,B |
| 原子数 atom_count | 106 |
XFFX
Cryo-Structural Insights into Enzymatic Peptide Self-Assembly Driving Extrinsic Lytic Cell Death.
J.Am.Chem.Soc. (2026)
Files (7)
- pr_distribution /app/data/pr_computation/nx/9nxz/pr_distribution.json
- pr_output /app/data/pr_computation/nx/9nxz/9nxz.pr.out
- pr_plot /app/data/visualization/pr_computation/nx/9nxz/9nxz_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/nx/9nxz/9nxz.dat
- saxs_fit /app/data/saxs_computation/nx/9nxz/9nxz.fit
- saxs_log /app/data/saxs_computation/nx/9nxz/9nxz.log
- saxs_plot /app/data/visualization/saxs_computation/nx/9nxz/9nxz_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/nx/9nxz/9nxz.fit |
| pddf |
/app/data/pr_computation/nx/9nxz/9nxz.pr.out |
| profile |
/app/data/saxs_computation/nx/9nxz/9nxz.dat |