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 | 9pgr |
| 沉积日期 deposition_date | 2025-07-08 |
| 结构标题 title | [18-7B G|A] 18 bp tensegrity triangle that propagates via blunt-end stacking with G stacking on A at the interface |
| 关键词 keywords | tensegrity triangle, DNA; DNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 15.19 Å |
| 回转半径 Rg (电子) rg_electron | 14.57 Å |
| 零角强度 I(0) i0 | 6066350.00 |
| 分子量 molecular_weight | 11031.0 kDa |
| 排除体积 excluded_volume | 10673 ų |
| 包络体积 envelope_volume | 14955 ų |
| 水化壳体积 shell_volume | 9380 ų |
| 包络直径 envelope_diameter | 48.1 Å |
| 壳层 Rg shell_rg | 19.08 Å |
| 包络 Rg envelope_rg | 14.46 Å |
| 形状 Rg shape_rg | 14.45 Å |
| 总 Rg total_rg | 15.34 Å |
| 总原子数 total_atoms | 732 |
| 残基数 n_residues | 36 |
| 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 | 47.5 Å |
| Rg (实空间) rg_real | 15.13 Å |
| Rg 误差 (实空间) rg_real_error | 0.21 Å |
| I(0) (实空间) i0_real | 6.0660e+06 |
| I(0) 误差 (实空间) i0_real_error | 6.6370e+04 |
| Rg (倒空间) rg_reciprocal | 15.13 Å |
| I(0) (倒空间) i0_reciprocal | 6066000.0000 |
| 解质量估计 total_estimate | 0.9125 |
| 解质量评级 solution_quality |
EXCELLENT
a EXCELLENT solution
|
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 46.3 Å |
| 偏度 Skewness skewness | 0.139 |
| 峰度 Kurtosis kurtosis | -0.526 |
| 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 | 280900.0000 |
| 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: 0.960;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.998;
Smooth: 0.980
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 109.404 Å |
| 晶胞边长 b length_b | 109.404 Å |
| 晶胞边长 c length_c | 50.056 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 | 120.00 ° |
| 晶胞分子数 Z z_pdb | 6 |
对称性 Symmetry
| 空间群 space_group | P 3 2 1 |
| 空间群编号 int_tables_number | 150 |
| 晶系 crystal_system | trigonal |
精修参数 Refinement
| 分辨率 resolution | 3.620 Å |
| 最低分辨率 resolution_low | 34.410 Å |
| R 因子 r_factor | 0.2487 |
| R_work r_work | 0.2476 |
| R_free r_free | 0.2694 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
; |
| 分子量 formula_weight | 2724.8 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 | E |
| 原子数 atom_count | 732 |
CGGACATCA
Entity 2
polymer
| 描述 description | ;DNA (5'-D(P*TP*AP*CP*AP*CP*CP*G)-3')
; |
| 分子量 formula_weight | 2082.4 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 | B |
TACACCG
Entity 3
polymer
| 描述 description | ;DNA (5'-D(*TP*GP*AP*TP*GP*TP*GP*GP*TP*GP*C)-3')
; |
| 分子量 formula_weight | 3420.2 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 | C |
TGATGTGGTGC
Entity 4
polymer
| 描述 description | ;DNA (5'-D(*GP*CP*AP*CP*CP*TP*GP*TP*A)-3')
; |
| 分子量 formula_weight | 2715.8 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 | A |
GCACCTGTA
Blunt-force assembly of programmable DNA architectures using pi-pi stacking.
Nat Commun (2026)
Files (7)
- pr_distribution /app/data/pr_computation/pg/9pgr/pr_distribution.json
- pr_output /app/data/pr_computation/pg/9pgr/9pgr.pr.out
- pr_plot /app/data/visualization/pr_computation/pg/9pgr/9pgr_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/pg/9pgr/9pgr.dat
- saxs_fit /app/data/saxs_computation/pg/9pgr/9pgr.fit
- saxs_log /app/data/saxs_computation/pg/9pgr/9pgr.log
- saxs_plot /app/data/visualization/saxs_computation/pg/9pgr/9pgr_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/pg/9pgr/9pgr.fit |
| pddf |
/app/data/pr_computation/pg/9pgr/9pgr.pr.out |
| profile |
/app/data/saxs_computation/pg/9pgr/9pgr.dat |