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 | 1f6c |
| 沉积日期 deposition_date | 2000-06-21 |
| 结构标题 title | CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE |
| 关键词 keywords | B-DNA, E-DNA, DOUBLE HELIX, DNA; DNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 17.58 Å |
| 回转半径 Rg (电子) rg_electron | 17.65 Å |
| 零角强度 I(0) i0 | 4150090.00 |
| 分子量 molecular_weight | 9290.0 kDa |
| 排除体积 excluded_volume | 9128 ų |
| 包络体积 envelope_volume | 13705 ų |
| 水化壳体积 shell_volume | 7868 ų |
| 包络直径 envelope_diameter | 64.5 Å |
| 壳层 Rg shell_rg | 20.47 Å |
| 包络 Rg envelope_rg | 18.19 Å |
| 形状 Rg shape_rg | 17.57 Å |
| 总 Rg total_rg | 18.13 Å |
| 总原子数 total_atoms | 621 |
| 残基数 n_residues | 30 |
| 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 | 65.5 Å |
| Rg (实空间) rg_real | 17.96 Å |
| Rg 误差 (实空间) rg_real_error | 0.83 Å |
| I(0) (实空间) i0_real | 4.1500e+06 |
| I(0) 误差 (实空间) i0_real_error | 6.4580e+04 |
| Rg (倒空间) rg_reciprocal | 17.91 Å |
| I(0) (倒空间) i0_reciprocal | 4150000.0000 |
| 解质量估计 total_estimate | 0.7655 |
| 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 | 14.8 Å |
| 偏度 Skewness skewness | 0.688 |
| 峰度 Kurtosis kurtosis | -0.036 |
| 角度范围 angular_range | — – 0.4550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 202200.0000 |
| 实空间数据点数 n_real_points | 76 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.591;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.180;
Smooth: 0.995
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 71.500 Å |
| 晶胞边长 b length_b | 71.500 Å |
| 晶胞边长 c length_c | 59.630 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 | 40 |
对称性 Symmetry
| 空间群 space_group | P 41 21 2 |
| 空间群编号 int_tables_number | 92 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 2.700 Å |
| 最低分辨率 resolution_low | 8.000 Å |
| R 因子 r_factor | 0.2320 |
| R_work r_work | 0.2260 |
| R_free r_free | 0.2880 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
; |
| 分子量 formula_weight | 1810.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 5 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | A,B,C,D,E |
| 原子数 atom_count | 637 |
GGCGCC
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 | 2 |
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 | 16 |
The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.
Nat.Struct.Biol. (2000)
Files (7)
- pr_distribution /app/data/pr_computation/f6/1f6c/pr_distribution.json
- pr_output /app/data/pr_computation/f6/1f6c/1f6c.pr.out
- pr_plot /app/data/visualization/pr_computation/f6/1f6c/1f6c_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/f6/1f6c/1f6c.dat
- saxs_fit /app/data/saxs_computation/f6/1f6c/1f6c.fit
- saxs_log /app/data/saxs_computation/f6/1f6c/1f6c.log
- saxs_plot /app/data/visualization/saxs_computation/f6/1f6c/1f6c_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/f6/1f6c/1f6c.fit |
| pddf |
/app/data/pr_computation/f6/1f6c/1f6c.pr.out |
| profile |
/app/data/saxs_computation/f6/1f6c/1f6c.dat |