SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
下载 Download
| 条目编号 entry_id | 2bee |
| 沉积日期 deposition_date | 2005-10-24 |
| 结构标题 title | Complex Between Paromomycin derivative JS4 and the 16S-Rrna A Site |
| 关键词 keywords | RNA-AMINOGLYCOSIDE INTERACTIONS, A SITE, UOU PAIRS, AA BULGES, RNA-antibiotic complex; RNA/antibiotic |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 17.87 Å |
| 回转半径 Rg (电子) rg_electron | 17.59 Å |
| 零角强度 I(0) i0 | 10947100.00 |
| 分子量 molecular_weight | 15050.0 kDa |
| 排除体积 excluded_volume | 14485 ų |
| 包络体积 envelope_volume | 20449 ų |
| 水化壳体积 shell_volume | 11020 ų |
| 包络直径 envelope_diameter | 62.8 Å |
| 壳层 Rg shell_rg | 21.87 Å |
| 包络 Rg envelope_rg | 17.62 Å |
| 形状 Rg shape_rg | 17.55 Å |
| 总 Rg total_rg | 18.12 Å |
| 总原子数 total_atoms | 996 |
| 残基数 n_residues | 42 |
| 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 | 61.6 Å |
| Rg (实空间) rg_real | 18.04 Å |
| Rg 误差 (实空间) rg_real_error | 0.55 Å |
| I(0) (实空间) i0_real | 1.0950e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.5410e+05 |
| Rg (倒空间) rg_reciprocal | 18.02 Å |
| I(0) (倒空间) i0_reciprocal | 10950000.0000 |
| 解质量估计 total_estimate | 0.8287 |
| 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 | 16.6 Å |
| 偏度 Skewness skewness | 0.524 |
| 峰度 Kurtosis kurtosis | -0.319 |
| 角度范围 angular_range | — – 0.4450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 956800.0000 |
| 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: 0.664;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.795;
Smooth: 0.980
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 39.171 Å |
| 晶胞边长 b length_b | 39.171 Å |
| 晶胞边长 c length_c | 99.027 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 41 |
| 空间群编号 int_tables_number | 76 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 2.600 Å |
| 最低分辨率 resolution_low | 30.000 Å |
| R 因子 r_factor | — |
| R_work r_work | 0.2200 |
| R_free r_free | 0.2600 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3' |
| 分子量 formula_weight | 7048.3 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 | 1059 |
CGCGUCACACCGGUGAAGUCGC
Entity 2
non-polymer
| 描述 description | ;(2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3R,4R,5S)-4-(2-(3-AMINOPROPYLAMINO)ETHOXY)-5-((1R,2R,3S,5R,6S)-3,5-DIAM INO-2-((2S,3R,4R,5S,6R)-3-AMINO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-( HYDROXYMETHYL)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL
; |
| 分子量 formula_weight | 715.8 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
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 | 63 |
Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site
ANGEW.CHEM.INT.ED.ENGL. (2004)
Files (7)
- pr_distribution /app/data/pr_computation/be/2bee/pr_distribution.json
- pr_output /app/data/pr_computation/be/2bee/2bee.pr.out
- pr_plot /app/data/visualization/pr_computation/be/2bee/2bee_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/be/2bee/2bee.dat
- saxs_fit /app/data/saxs_computation/be/2bee/2bee.fit
- saxs_log /app/data/saxs_computation/be/2bee/2bee.log
- saxs_plot /app/data/visualization/saxs_computation/be/2bee/2bee_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/be/2bee/2bee.fit |
| pddf |
/app/data/pr_computation/be/2bee/2bee.pr.out |
| profile |
/app/data/saxs_computation/be/2bee/2bee.dat |