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 | 8skw |
| 沉积日期 deposition_date | 2023-04-20 |
| 结构标题 title | MicroED structure of d(CGCGCG)2 Z-DNA |
| 关键词 keywords | Z-DNA, DNA; DNA |
| 实验方法 method | ELECTRON CRYSTALLOGRAPHY |
| 回转半径 Rg (Guinier) rg_guinier | 9.46 Å |
| 回转半径 Rg (电子) rg_electron | 8.70 Å |
| 零角强度 I(0) i0 | 795708.00 |
| 分子量 molecular_weight | 3797.0 kDa |
| 排除体积 excluded_volume | 3773 ų |
| 包络体积 envelope_volume | 4554 ų |
| 水化壳体积 shell_volume | 4964 ų |
| 包络直径 envelope_diameter | 27.8 Å |
| 壳层 Rg shell_rg | 13.05 Å |
| 包络 Rg envelope_rg | 8.88 Å |
| 形状 Rg shape_rg | 8.67 Å |
| 总 Rg total_rg | 9.73 Å |
| 总原子数 total_atoms | 414 |
| 残基数 n_residues | 12 |
| 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 | 30.5 Å |
| Rg (实空间) rg_real | 9.41 Å |
| Rg 误差 (实空间) rg_real_error | 0.23 Å |
| I(0) (实空间) i0_real | 7.9570e+05 |
| I(0) 误差 (实空间) i0_real_error | 7.5210e+03 |
| Rg (倒空间) rg_reciprocal | 9.41 Å |
| I(0) (倒空间) i0_reciprocal | 795700.0000 |
| 解质量估计 total_estimate | 0.8922 |
| 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 | 12.4 Å |
| 偏度 Skewness skewness | 0.170 |
| 峰度 Kurtosis kurtosis | -0.302 |
| 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 | 50390.0000 |
| 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: 0.877;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 1.000;
Smooth: 0.965
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 18.280 Å |
| 晶胞边长 b length_b | 32.000 Å |
| 晶胞边长 c length_c | 41.670 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 | 8 |
对称性 Symmetry
| 空间群 space_group | P 21 21 21 |
| 空间群编号 int_tables_number | 19 |
| 晶系 crystal_system | orthorhombic |
精修参数 Refinement
| 分辨率 resolution | 1.100 Å |
| 最低分辨率 resolution_low | 25.380 Å |
| R 因子 r_factor | 0.2105 |
| R_work r_work | 0.2098 |
| R_free r_free | 0.2257 |
冷冻电镜 EM 3D
| 分辨率 resolution | 1.10 Å |
| 分辨率测定方法 resolution_method | — |
| 颗粒数 num_particles | — |
Entity 1
polymer
| 描述 description | ;DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
; |
| 分子量 formula_weight | 1810.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | B,A |
| 原子数 atom_count | 505 |
CGCGCG
Entity 2
non-polymer
| 描述 description | SPERMINE |
| 分子量 formula_weight | 202.3 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
Entity 3
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 | 33 |
Structure determination of a DNA crystal by MicroED.
Structure (2023)
Files (7)
- pr_distribution /app/data/pr_computation/sk/8skw/pr_distribution.json
- pr_output /app/data/pr_computation/sk/8skw/8skw.pr.out
- pr_plot /app/data/visualization/pr_computation/sk/8skw/8skw_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/sk/8skw/8skw.dat
- saxs_fit /app/data/saxs_computation/sk/8skw/8skw.fit
- saxs_log /app/data/saxs_computation/sk/8skw/8skw.log
- saxs_plot /app/data/visualization/saxs_computation/sk/8skw/8skw_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/sk/8skw/8skw.fit |
| pddf |
/app/data/pr_computation/sk/8skw/8skw.pr.out |
| profile |
/app/data/saxs_computation/sk/8skw/8skw.dat |