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 | 8fb4 |
| 沉积日期 deposition_date | 2022-11-29 |
| 结构标题 title | ;Structure of an alternating AT 16-mer bound by diamidine DB1476: 5'-GCTGGATATATCCAGC-3
; |
| 关键词 keywords | DNA, AT sequence, Minor groove; DNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 19.34 Å |
| 回转半径 Rg (电子) rg_electron | 18.89 Å |
| 零角强度 I(0) i0 | 10877100.00 |
| 分子量 molecular_weight | 15996.0 kDa |
| 排除体积 excluded_volume | 15930 ų |
| 包络体积 envelope_volume | 24405 ų |
| 水化壳体积 shell_volume | 11618 ų |
| 包络直径 envelope_diameter | 64.0 Å |
| 壳层 Rg shell_rg | 23.53 Å |
| 包络 Rg envelope_rg | 18.57 Å |
| 形状 Rg shape_rg | 18.81 Å |
| 总 Rg total_rg | 19.52 Å |
| 总原子数 total_atoms | 1630 |
| 残基数 n_residues | 48 |
| 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 | 67.2 Å |
| Rg (实空间) rg_real | 19.35 Å |
| Rg 误差 (实空间) rg_real_error | 0.49 Å |
| I(0) (实空间) i0_real | 1.0880e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.4980e+05 |
| Rg (倒空间) rg_reciprocal | 19.35 Å |
| I(0) (倒空间) i0_reciprocal | 10880000.0000 |
| 解质量估计 total_estimate | 0.8769 |
| 解质量评级 solution_quality |
GOOD
a GOOD solution
|
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 26.5 Å |
| 偏度 Skewness skewness | 0.234 |
| 峰度 Kurtosis kurtosis | -0.532 |
| 角度范围 angular_range | — – 0.4100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 579300.0000 |
| 实空间数据点数 n_real_points | 72 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.857;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.823;
Smooth: 1.000
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 38.730 Å |
| 晶胞边长 b length_b | 38.730 Å |
| 晶胞边长 c length_c | 160.394 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 | 18 |
对称性 Symmetry
| 空间群 space_group | P 31 2 1 |
| 空间群编号 int_tables_number | 152 |
| 晶系 crystal_system | trigonal |
精修参数 Refinement
| 分辨率 resolution | 1.490 Å |
| 最低分辨率 resolution_low | 28.410 Å |
| R 因子 r_factor | 0.2609 |
| R_work r_work | 0.2579 |
| R_free r_free | 0.2947 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA (5'-D(*GP*CP*TP*GP*GP*AP*TP*AP*TP*AP*TP*CP*CP*AP*GP*C)-3')
; |
| 分子量 formula_weight | 4898.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 3 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | A,B,C |
| 原子数 atom_count | 1779 |
GCTGGATATATCCAGC
Entity 2
non-polymer
| 描述 description | 4,4'-(1H-benzimidazole-2,6-diyl)di(benzene-1-carboximidamide) |
| 分子量 formula_weight | 354.4 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
Entity 3
non-polymer
| 描述 description | CALCIUM ION |
| 分子量 formula_weight | 40.1 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 15 |
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 | 149 |
X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.
Acs Bio Med Chem Au (2023)
Files (7)
- pr_distribution /app/data/pr_computation/fb/8fb4/pr_distribution.json
- pr_output /app/data/pr_computation/fb/8fb4/8fb4.pr.out
- pr_plot /app/data/visualization/pr_computation/fb/8fb4/8fb4_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/fb/8fb4/8fb4.dat
- saxs_fit /app/data/saxs_computation/fb/8fb4/8fb4.fit
- saxs_log /app/data/saxs_computation/fb/8fb4/8fb4.log
- saxs_plot /app/data/visualization/saxs_computation/fb/8fb4/8fb4_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/fb/8fb4/8fb4.fit |
| pddf |
/app/data/pr_computation/fb/8fb4/8fb4.pr.out |
| profile |
/app/data/saxs_computation/fb/8fb4/8fb4.dat |