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 | 1g3v |
| 沉积日期 deposition_date | 2000-10-25 |
| 结构标题 title | CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2 |
| 关键词 keywords | nickel binding, B-DNA, DNA; DNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 18.02 Å |
| 回转半径 Rg (电子) rg_electron | 17.87 Å |
| 零角强度 I(0) i0 | 7295280.00 |
| 分子量 molecular_weight | 12068.0 kDa |
| 排除体积 excluded_volume | 11449 ų |
| 包络体积 envelope_volume | 16890 ų |
| 水化壳体积 shell_volume | 9434 ų |
| 包络直径 envelope_diameter | 66.2 Å |
| 壳层 Rg shell_rg | 20.91 Å |
| 包络 Rg envelope_rg | 18.17 Å |
| 形状 Rg shape_rg | 17.60 Å |
| 总 Rg total_rg | 18.57 Å |
| 总原子数 total_atoms | 777 |
| 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 | 66.6 Å |
| Rg (实空间) rg_real | 18.36 Å |
| Rg 误差 (实空间) rg_real_error | 0.60 Å |
| I(0) (实空间) i0_real | 7.2950e+06 |
| I(0) 误差 (实空间) i0_real_error | 8.9360e+04 |
| Rg (倒空间) rg_reciprocal | 18.32 Å |
| I(0) (倒空间) i0_reciprocal | 7295000.0000 |
| 解质量估计 total_estimate | 0.7719 |
| 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 | 16.2 Å |
| 偏度 Skewness skewness | 0.670 |
| 峰度 Kurtosis kurtosis | -0.078 |
| 角度范围 angular_range | — – 0.4400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 499400.0000 |
| 实空间数据点数 n_real_points | 75 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.560;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.364;
Smooth: 0.985
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 53.031 Å |
| 晶胞边长 b length_b | 53.031 Å |
| 晶胞边长 c length_c | 97.787 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 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 | 3.100 Å |
| 最低分辨率 resolution_low | 8.000 Å |
| R 因子 r_factor | — |
| R_work r_work | 0.2090 |
| R_free r_free | 0.2700 |
Entity 1
polymer
| 描述 description | 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3' |
| 分子量 formula_weight | 3045.0 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,B,C,D |
| 原子数 atom_count | 829 |
CGTGTACACG
Entity 2
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 | 8 |
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 | 52 |
Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2.
J.Biol.Inorg.Chem. (2002)
Files (7)
- pr_distribution /app/data/pr_computation/g3/1g3v/pr_distribution.json
- pr_output /app/data/pr_computation/g3/1g3v/1g3v.pr.out
- pr_plot /app/data/visualization/pr_computation/g3/1g3v/1g3v_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/g3/1g3v/1g3v.dat
- saxs_fit /app/data/saxs_computation/g3/1g3v/1g3v.fit
- saxs_log /app/data/saxs_computation/g3/1g3v/1g3v.log
- saxs_plot /app/data/visualization/saxs_computation/g3/1g3v/1g3v_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/g3/1g3v/1g3v.fit |
| pddf |
/app/data/pr_computation/g3/1g3v/1g3v.pr.out |
| profile |
/app/data/saxs_computation/g3/1g3v/1g3v.dat |