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 | 9kzp |
| 沉积日期 deposition_date | 2024-12-11 |
| 结构标题 title | Z-form DNA-RNA hybrid in dynamic simulation |
| 关键词 keywords | Z-form DNA-RNA hybrid, dynamic simulation, Okazaki fragment, block DNA replication, DNA-RNA complex; DNA/RNA |
| 实验方法 method | SOLUTION NMR |
| 回转半径 Rg (Guinier) rg_guinier | 10.31 Å |
| 回转半径 Rg (电子) rg_electron | 10.49 Å |
| 零角强度 I(0) i0 | 102108000.00 |
| 分子量 molecular_weight | 50044.0 kDa |
| 排除体积 excluded_volume | 48169 ų |
| 包络体积 envelope_volume | 6470 ų |
| 水化壳体积 shell_volume | 5930 ų |
| 包络直径 envelope_diameter | 37.0 Å |
| 壳层 Rg shell_rg | 14.80 Å |
| 包络 Rg envelope_rg | 10.82 Å |
| 形状 Rg shape_rg | 10.48 Å |
| 总 Rg total_rg | 10.61 Å |
| 总原子数 total_atoms | 5110 |
| 残基数 n_residues | 120 |
| 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 | 33.6 Å |
| Rg (实空间) rg_real | 10.36 Å |
| Rg 误差 (实空间) rg_real_error | 0.35 Å |
| I(0) (实空间) i0_real | 1.0210e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1100e+06 |
| Rg (倒空间) rg_reciprocal | 10.36 Å |
| I(0) (倒空间) i0_reciprocal | 102100000.0000 |
| 解质量估计 total_estimate | 0.8645 |
| 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 | 11.9 Å |
| 偏度 Skewness skewness | 0.462 |
| 峰度 Kurtosis kurtosis | -0.197 |
| 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 | 66440.0000 |
| 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: 0.792;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.964;
Smooth: 0.894
|
Entity 1
polymer
| 描述 description | ;DNA (5'-D(*(5CM)P*GP*(5CM)P*AP*(5CM)P*GP*(5CM)P*G)-3')
; |
| 分子量 formula_weight | 2468.7 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | D |
| 原子数 atom_count | 5110 |
CGCACGCG
Entity 2
polymer
| 描述 description | ;RNA (5'-R(*CP*GP*CP*GP*UP*GP*CP*G)-3')
; |
| 分子量 formula_weight | 2557.6 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polyribonucleotide |
| 链编号 strand_id | R |
CGCGUGCG
Z-form DNA-RNA hybrid blocks DNA replication.
Nucleic Acids Res. (2025)
Files (7)
- pr_distribution /app/data/pr_computation/kz/9kzp/pr_distribution.json
- pr_output /app/data/pr_computation/kz/9kzp/9kzp.pr.out
- pr_plot /app/data/visualization/pr_computation/kz/9kzp/9kzp_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/kz/9kzp/9kzp.dat
- saxs_fit /app/data/saxs_computation/kz/9kzp/9kzp.fit
- saxs_log /app/data/saxs_computation/kz/9kzp/9kzp.log
- saxs_plot /app/data/visualization/saxs_computation/kz/9kzp/9kzp_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/kz/9kzp/9kzp.fit |
| pddf |
/app/data/pr_computation/kz/9kzp/9kzp.pr.out |
| profile |
/app/data/saxs_computation/kz/9kzp/9kzp.dat |