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 | 9mmd |
| 沉积日期 deposition_date | 2024-12-20 |
| 最后修订 last_revision | 2025-10-29 |
| 结构标题 title | ;[T:Ag+/Hg2+:T--(pH9.5-pH11; 21s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 9.5 and soaked in pH 11 with Ag+ and Hg2+ for 21s
; |
| 关键词 keywords | Tensegrity triangle, metal-mediated DNA, DNA; DNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 20.99 Å |
| 回转半径 Rg (电子) rg_electron | 21.30 Å |
| 零角强度 I(0) i0 | 8426820.00 |
| 分子量 molecular_weight | 13178.0 kDa |
| 排除体积 excluded_volume | 12612 ų |
| 包络体积 envelope_volume | 20487 ų |
| 水化壳体积 shell_volume | 9830 ų |
| 包络直径 envelope_diameter | 72.1 Å |
| 壳层 Rg shell_rg | 23.83 Å |
| 包络 Rg envelope_rg | 21.49 Å |
| 形状 Rg shape_rg | 21.35 Å |
| 总 Rg total_rg | 21.50 Å |
| 总原子数 total_atoms | 860 |
| 残基数 n_residues | 42 |
| 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 | 74.6 Å |
| Rg (实空间) rg_real | 21.44 Å |
| Rg 误差 (实空间) rg_real_error | 0.79 Å |
| I(0) (实空间) i0_real | 8.4270e+06 |
| I(0) 误差 (实空间) i0_real_error | 1.1840e+05 |
| Rg (倒空间) rg_reciprocal | 21.36 Å |
| I(0) (倒空间) i0_reciprocal | 8426000.0000 |
| 解质量估计 total_estimate | 0.6913 |
| 解质量评级 solution_quality |
REASONABLE
a REASONABLE solution
|
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 16.2 Å |
| 偏度 Skewness skewness | 0.639 |
| 峰度 Kurtosis kurtosis | -0.365 |
| 角度范围 angular_range | — – 0.3800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 654500.0000 |
| 实空间数据点数 n_real_points | 70 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.343;
Stabil: 0.979;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.136;
Smooth: 0.882
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 105.670 Å |
| 晶胞边长 b length_b | 105.670 Å |
| 晶胞边长 c length_c | 95.010 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 | 9 |
对称性 Symmetry
| 空间群 space_group | H 3 |
| 空间群编号 int_tables_number | 146 |
| 晶系 crystal_system | trigonal |
精修参数 Refinement
| 分辨率 resolution | 5.030 Å |
| 最低分辨率 resolution_low | 19.970 Å |
| R 因子 r_factor | 0.1990 |
| R_work r_work | 0.1982 |
| R_free r_free | 0.2060 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
; |
| 分子量 formula_weight | 6463.2 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 | A |
| 原子数 atom_count | 860 |
GAGCAGCCTGTTTGGACATCA
Entity 2
polymer
| 描述 description | ;DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3')
; |
| 分子量 formula_weight | 2066.4 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 |
CCATACA
Entity 3
polymer
| 描述 description | ;DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
; |
| 分子量 formula_weight | 2129.4 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 | C |
GGCTGCT
Entity 4
polymer
| 描述 description | ;DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
; |
| 分子量 formula_weight | 2128.4 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 | D |
CTGATGT
Entity 5
non-polymer
| 描述 description | SILVER ION |
| 分子量 formula_weight | 107.9 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
Transmetalation for DNA-Based Molecular Electronics.
Small (2025)
Files (7)
- pr_distribution /app/data/pr_computation/mm/9mmd/pr_distribution.json
- pr_output /app/data/pr_computation/mm/9mmd/9mmd.pr.out
- pr_plot /app/data/visualization/pr_computation/mm/9mmd/9mmd_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/mm/9mmd/9mmd.dat
- saxs_fit /app/data/saxs_computation/mm/9mmd/9mmd.fit
- saxs_log /app/data/saxs_computation/mm/9mmd/9mmd.log
- saxs_plot /app/data/visualization/saxs_computation/mm/9mmd/9mmd_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/mm/9mmd/9mmd.fit |
| pddf |
/app/data/pr_computation/mm/9mmd/9mmd.pr.out |
| profile |
/app/data/saxs_computation/mm/9mmd/9mmd.dat |