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 | 2grb |
| 沉积日期 deposition_date | 2006-04-24 |
| 结构标题 title | Crystal Structure of an RNA Quadruplex Containing Inosine-tetrad |
| 关键词 keywords | RNA Quadruplex, RNA; RNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 14.20 Å |
| 回转半径 Rg (电子) rg_electron | 13.56 Å |
| 零角强度 I(0) i0 | 11172300.00 |
| 分子量 molecular_weight | 15405.0 kDa |
| 排除体积 excluded_volume | 14736 ų |
| 包络体积 envelope_volume | 17628 ų |
| 水化壳体积 shell_volume | 11221 ų |
| 包络直径 envelope_diameter | 46.8 Å |
| 壳层 Rg shell_rg | 19.06 Å |
| 包络 Rg envelope_rg | 13.86 Å |
| 形状 Rg shape_rg | 13.37 Å |
| 总 Rg total_rg | 14.49 Å |
| 总原子数 total_atoms | 982 |
| 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 | 44.7 Å |
| Rg (实空间) rg_real | 14.31 Å |
| Rg 误差 (实空间) rg_real_error | 0.08 Å |
| I(0) (实空间) i0_real | 1.0950e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.4320e+04 |
| Rg (倒空间) rg_reciprocal | 14.15 Å |
| I(0) (倒空间) i0_reciprocal | 11170000.0000 |
| 解质量估计 total_estimate | 0.6902 |
| 解质量评级 solution_quality |
REASONABLE
a REASONABLE solution
|
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 17.0 Å |
| 偏度 Skewness skewness | 0.343 |
| 峰度 Kurtosis kurtosis | -0.250 |
| 角度范围 angular_range | — – 0.5000 Å−1 |
| 当前正则化参数 α current_alpha | 9.4820 |
| 最高正则化参数 α highest_alpha | 3190000.0000 |
| 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: 0.905;
Stabil: 0.936;
Sysdev: 0.000;
Positv: 1.000;
Valcen: 1.000;
Smooth: 0.472
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 29.060 Å |
| 晶胞边长 b length_b | 52.738 Å |
| 晶胞边长 c length_c | 37.344 Å |
| 晶胞夹角 α angle_alpha | 90.00 ° |
| 晶胞夹角 β angle_beta | 102.98 ° |
| 晶胞夹角 γ angle_gamma | 90.00 ° |
| 晶胞分子数 Z z_pdb | 16 |
对称性 Symmetry
| 空间群 space_group | P 1 21 1 |
| 空间群编号 int_tables_number | 4 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 1.400 Å |
| 最低分辨率 resolution_low | 8.000 Å |
| R 因子 r_factor | 0.1978 |
| R_work r_work | 0.1951 |
| R_free r_free | 0.2500 |
Entity 1
polymer
| 描述 description | 5'-R(*(U33)P*GP*IP*GP*GP*U)-3' |
| 分子量 formula_weight | 1916.1 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 8 |
聚合体 Polymer
| 聚合体类型 type | polyribonucleotide |
| 链编号 strand_id | A,B,C,D,E,F,G,H |
| 原子数 atom_count | 1160 |
UGIGGU
Entity 2
non-polymer
| 描述 description | POTASSIUM ION |
| 分子量 formula_weight | 39.1 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 11 |
Entity 3
non-polymer
| 描述 description | STRONTIUM ION |
| 分子量 formula_weight | 87.6 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
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 | 178 |
Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads.
J.Mol.Biol. (2006)
Files (7)
- pr_distribution /app/data/pr_computation/gr/2grb/pr_distribution.json
- pr_output /app/data/pr_computation/gr/2grb/2grb.pr.out
- pr_plot /app/data/visualization/pr_computation/gr/2grb/2grb_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/gr/2grb/2grb.dat
- saxs_fit /app/data/saxs_computation/gr/2grb/2grb.fit
- saxs_log /app/data/saxs_computation/gr/2grb/2grb.log
- saxs_plot /app/data/visualization/saxs_computation/gr/2grb/2grb_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/gr/2grb/2grb.fit |
| pddf |
/app/data/pr_computation/gr/2grb/2grb.pr.out |
| profile |
/app/data/saxs_computation/gr/2grb/2grb.dat |