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 | 1kd5 |
| 沉积日期 deposition_date | 2001-11-12 |
| 结构标题 title | The Crystal Structure of r(GGUCACAGCCC)2 metal free form |
| 关键词 keywords | RNA duplex, RNA; RNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 13.56 Å |
| 回转半径 Rg (电子) rg_electron | 13.20 Å |
| 零角强度 I(0) i0 | 2683740.00 |
| 分子量 molecular_weight | 6946.0 kDa |
| 排除体积 excluded_volume | 6555 ų |
| 包络体积 envelope_volume | 9070 ų |
| 水化壳体积 shell_volume | 6793 ų |
| 包络直径 envelope_diameter | 48.6 Å |
| 壳层 Rg shell_rg | 17.07 Å |
| 包络 Rg envelope_rg | 13.31 Å |
| 形状 Rg shape_rg | 13.09 Å |
| 总 Rg total_rg | 13.95 Å |
| 总原子数 total_atoms | 460 |
| 残基数 n_residues | 22 |
| 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 | 51.0 Å |
| Rg (实空间) rg_real | 13.67 Å |
| Rg 误差 (实空间) rg_real_error | 0.46 Å |
| I(0) (实空间) i0_real | 2.6840e+06 |
| I(0) 误差 (实空间) i0_real_error | 3.1670e+04 |
| Rg (倒空间) rg_reciprocal | 13.67 Å |
| I(0) (倒空间) i0_reciprocal | 2684000.0000 |
| 解质量估计 total_estimate | 0.7822 |
| 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 | 14.9 Å |
| 偏度 Skewness skewness | 0.545 |
| 峰度 Kurtosis kurtosis | -0.113 |
| 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 | 161400.0000 |
| 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: 0.533;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.572;
Smooth: 0.994
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 45.388 Å |
| 晶胞边长 b length_b | 45.388 Å |
| 晶胞边长 c length_c | 51.499 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 43 |
| 空间群编号 int_tables_number | 78 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 1.580 Å |
| 最低分辨率 resolution_low | 5.000 Å |
| R 因子 r_factor | 0.1714 |
| R_work r_work | 0.1714 |
| R_free r_free | 0.2260 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3' |
| 分子量 formula_weight | 3481.1 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
聚合体 Polymer
| 聚合体类型 type | polyribonucleotide |
| 链编号 strand_id | A,B |
| 原子数 atom_count | 587 |
GGUCACAGCCC
Entity 2
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 | 127 |
Crystal structures of r(GGUCACAGCCC)2.
Acta Crystallogr.,Sect.D (2003)
Files (7)
- pr_distribution /app/data/pr_computation/kd/1kd5/pr_distribution.json
- pr_output /app/data/pr_computation/kd/1kd5/1kd5.pr.out
- pr_plot /app/data/visualization/pr_computation/kd/1kd5/1kd5_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/kd/1kd5/1kd5.dat
- saxs_fit /app/data/saxs_computation/kd/1kd5/1kd5.fit
- saxs_log /app/data/saxs_computation/kd/1kd5/1kd5.log
- saxs_plot /app/data/visualization/saxs_computation/kd/1kd5/1kd5_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/kd/1kd5/1kd5.fit |
| pddf |
/app/data/pr_computation/kd/1kd5/1kd5.pr.out |
| profile |
/app/data/saxs_computation/kd/1kd5/1kd5.dat |