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 | 2adw |
| 沉积日期 deposition_date | 2005-07-21 |
| 结构标题 title | Crystal structure of Echinomycin-(ACGTACGT)2 solved by SAD |
| 关键词 keywords | DNA-ANTIBIOTIC COMPLEX, BISINTERCALATOR, HOOGSTEEN BASEPAIR, DEPSIPEPTIDE, QUINOXALINE, THIOACETAL, ANTIBIOTIC, ANTITUMOR; DNA/ANTIBIOTIC |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 23.70 Å |
| 回转半径 Rg (电子) rg_electron | 24.31 Å |
| 零角强度 I(0) i0 | 7314060.00 |
| 分子量 molecular_weight | 14302.0 kDa |
| 排除体积 excluded_volume | 15177 ų |
| 包络体积 envelope_volume | 19496 ų |
| 水化壳体积 shell_volume | 8909 ų |
| 包络直径 envelope_diameter | 86.6 Å |
| 壳层 Rg shell_rg | 25.05 Å |
| 包络 Rg envelope_rg | 24.80 Å |
| 形状 Rg shape_rg | 24.25 Å |
| 总 Rg total_rg | 24.50 Å |
| 总原子数 total_atoms | 1565 |
| 残基数 n_residues | 40 |
| 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 | 84.7 Å |
| Rg (实空间) rg_real | 24.39 Å |
| Rg 误差 (实空间) rg_real_error | 0.96 Å |
| I(0) (实空间) i0_real | 7.3140e+06 |
| I(0) 误差 (实空间) i0_real_error | 1.0880e+05 |
| Rg (倒空间) rg_reciprocal | 24.23 Å |
| I(0) (倒空间) i0_reciprocal | 7313000.0000 |
| 解质量估计 total_estimate | 0.6592 |
| 解质量评级 solution_quality |
REASONABLE
a REASONABLE solution
|
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 13.2 Å |
| 偏度 Skewness skewness | 0.666 |
| 峰度 Kurtosis kurtosis | -0.404 |
| 角度范围 angular_range | — – 0.3350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 157200.0000 |
| 实空间数据点数 n_real_points | 65 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.228;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.019;
Smooth: 0.863
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 80.904 Å |
| 晶胞边长 b length_b | 80.904 Å |
| 晶胞边长 c length_c | 48.194 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 | 32 |
对称性 Symmetry
| 空间群 space_group | P 42 21 2 |
| 空间群编号 int_tables_number | 94 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 1.600 Å |
| 最低分辨率 resolution_low | 30.000 Å |
| R 因子 r_factor | 0.1800 |
| R_work r_work | — |
| R_free r_free | 0.2210 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3' |
| 分子量 formula_weight | 2426.6 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 4 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | A,C,E,G |
| 原子数 atom_count | 1826 |
ACGTACGT
Entity 2
polymer
| 描述 description | ECHINOMYCIN |
| 分子量 formula_weight | 809.0 kDa |
| 来源方法 src_method | nat |
| 拷贝数 entity_count | 4 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | H,I,J,K |
SAXVSAXV
Entity 3
non-polymer
| 描述 description | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID |
| 分子量 formula_weight | 195.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
Entity 4
non-polymer
| 描述 description | NICKEL (II) ION |
| 分子量 formula_weight | 58.7 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
Entity 5
non-polymer
| 描述 description | ZINC ION |
| 分子量 formula_weight | 65.4 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
Entity 6
non-polymer
| 描述 description | 2-CARBOXYQUINOXALINE |
| 分子量 formula_weight | 174.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 8 |
Entity 7
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 | 86 |
Serendipitous Sad Phasing of an Echinomycin-(Acgtacgt)2 Bisintercalation Complex.
Acta Crystallogr.,Sect.D (2006)
Files (7)
- pr_distribution /app/data/pr_computation/ad/2adw/pr_distribution.json
- pr_output /app/data/pr_computation/ad/2adw/2adw.pr.out
- pr_plot /app/data/visualization/pr_computation/ad/2adw/2adw_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/ad/2adw/2adw.dat
- saxs_fit /app/data/saxs_computation/ad/2adw/2adw.fit
- saxs_log /app/data/saxs_computation/ad/2adw/2adw.log
- saxs_plot /app/data/visualization/saxs_computation/ad/2adw/2adw_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/ad/2adw/2adw.fit |
| pddf |
/app/data/pr_computation/ad/2adw/2adw.pr.out |
| profile |
/app/data/saxs_computation/ad/2adw/2adw.dat |