SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
下载 Download
| 条目编号 entry_id | 9k8o |
| 沉积日期 deposition_date | 2024-10-24 |
| 结构标题 title | Crystal structure of a short zinc-dependent DNAzyme minGAA |
| 关键词 keywords | DNAzyme, RNA cleavage, Zinc-dependent, DNA-RNA HYBRID; DNA-RNA HYBRID |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 33.71 Å |
| 回转半径 Rg (电子) rg_electron | 34.62 Å |
| 零角强度 I(0) i0 | 28187500.00 |
| 分子量 molecular_weight | 25125.0 kDa |
| 排除体积 excluded_volume | 24113 ų |
| 包络体积 envelope_volume | 43426 ų |
| 水化壳体积 shell_volume | 12978 ų |
| 包络直径 envelope_diameter | 122.1 Å |
| 壳层 Rg shell_rg | 32.55 Å |
| 包络 Rg envelope_rg | 34.68 Å |
| 形状 Rg shape_rg | 34.60 Å |
| 总 Rg total_rg | 34.54 Å |
| 总原子数 total_atoms | 1661 |
| 残基数 n_residues | 79 |
| 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 | 123.0 Å |
| Rg (实空间) rg_real | 34.45 Å |
| Rg 误差 (实空间) rg_real_error | 1.88 Å |
| I(0) (实空间) i0_real | 2.8190e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.6840e+05 |
| Rg (倒空间) rg_reciprocal | 33.99 Å |
| I(0) (倒空间) i0_reciprocal | 28180000.0000 |
| 解质量估计 total_estimate | 0.6243 |
| 解质量评级 solution_quality |
REASONABLE
a REASONABLE solution
|
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 18.3 Å |
| 偏度 Skewness skewness | 0.608 |
| 峰度 Kurtosis kurtosis | -0.543 |
| 角度范围 angular_range | — – 0.2350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 348400.0000 |
| 实空间数据点数 n_real_points | 48 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.118;
Stabil: 0.998;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.013;
Smooth: 0.750
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 38.861 Å |
| 晶胞边长 b length_b | 81.881 Å |
| 晶胞边长 c length_c | 81.776 Å |
| 晶胞夹角 α angle_alpha | 90.00 ° |
| 晶胞夹角 β angle_beta | 90.00 ° |
| 晶胞夹角 γ angle_gamma | 90.00 ° |
| 晶胞分子数 Z z_pdb | 16 |
对称性 Symmetry
| 空间群 space_group | P 2 21 21 |
| 空间群编号 int_tables_number | 18 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 3.040 Å |
| 最低分辨率 resolution_low | 40.940 Å |
| R 因子 r_factor | 0.2099 |
| R_work r_work | 0.2054 |
| R_free r_free | 0.2973 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | DNAzyme minGAA, catalytic strand |
| 分子量 formula_weight | 2990.0 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 4 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | A,C,E,G |
| 原子数 atom_count | 1685 |
GATCACCCGC
Entity 2
polymer
| 描述 description | substrate strand for DNAzyme minGAA |
| 分子量 formula_weight | 3485.3 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 4 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide/polyribonucleotide hybrid |
| 链编号 strand_id | B,D,F,H |
GCGGAAGGATC
Entity 3
non-polymer
| 描述 description | ZINC ION |
| 分子量 formula_weight | 65.4 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 3 |
Entity 4
water
| 描述 description | water |
| 分子量 formula_weight | 18.0 kDa |
| 来源方法 src_method | nat |
| 拷贝数 entity_count | 23 |
A minimal RNA-cleaving DNAzyme and its catalytic mechanism.
Nucleic Acids Res. (2026)
Files (7)
- pr_distribution /app/data/pr_computation/k8/9k8o/pr_distribution.json
- pr_output /app/data/pr_computation/k8/9k8o/9k8o.pr.out
- pr_plot /app/data/visualization/pr_computation/k8/9k8o/9k8o_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/k8/9k8o/9k8o.dat
- saxs_fit /app/data/saxs_computation/k8/9k8o/9k8o.fit
- saxs_log /app/data/saxs_computation/k8/9k8o/9k8o.log
- saxs_plot /app/data/visualization/saxs_computation/k8/9k8o/9k8o_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/k8/9k8o/9k8o.fit |
| pddf |
/app/data/pr_computation/k8/9k8o/9k8o.pr.out |
| profile |
/app/data/saxs_computation/k8/9k8o/9k8o.dat |