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 | 8sy1 |
| 沉积日期 deposition_date | 2023-05-24 |
| 结构标题 title | RNA duplex bound with imidazolium bridged GA dinucleotide |
| 关键词 keywords | RNA, imidazolium bridged GA dinucleotide; RNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 24.87 Å |
| 回转半径 Rg (电子) rg_electron | 25.44 Å |
| 零角强度 I(0) i0 | 19430900.00 |
| 分子量 molecular_weight | 20253.0 kDa |
| 排除体积 excluded_volume | 19331 ų |
| 包络体积 envelope_volume | 32100 ų |
| 水化壳体积 shell_volume | 12603 ų |
| 包络直径 envelope_diameter | 92.8 Å |
| 壳层 Rg shell_rg | 28.14 Å |
| 包络 Rg envelope_rg | 25.28 Å |
| 形状 Rg shape_rg | 25.39 Å |
| 总 Rg total_rg | 25.74 Å |
| 总原子数 total_atoms | 1344 |
| 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 | 88.4 Å |
| Rg (实空间) rg_real | 25.48 Å |
| Rg 误差 (实空间) rg_real_error | 1.04 Å |
| I(0) (实空间) i0_real | 1.9430e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.9600e+05 |
| Rg (倒空间) rg_reciprocal | 25.34 Å |
| I(0) (倒空间) i0_reciprocal | 19430000.0000 |
| 解质量估计 total_estimate | 0.6462 |
| 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 | 18.2 Å |
| 偏度 Skewness skewness | 0.647 |
| 峰度 Kurtosis kurtosis | -0.316 |
| 角度范围 angular_range | — – 0.3200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 970100.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.429;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.109;
Smooth: 0.000
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 43.656 Å |
| 晶胞边长 b length_b | 43.656 Å |
| 晶胞边长 c length_c | 81.126 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 | 120.00 ° |
| 晶胞分子数 Z z_pdb | 12 |
对称性 Symmetry
| 空间群 space_group | P 3 |
| 空间群编号 int_tables_number | 143 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 1.760 Å |
| 最低分辨率 resolution_low | 34.290 Å |
| R 因子 r_factor | 0.2254 |
| R_work r_work | 0.2238 |
| R_free r_free | 0.2563 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
; |
| 分子量 formula_weight | 4513.8 kDa |
| 来源方法 src_method | nat |
| 拷贝数 entity_count | 4 |
聚合体 Polymer
| 聚合体类型 type | polyribonucleotide |
| 链编号 strand_id | A,B,C,D |
| 原子数 atom_count | 1400 |
UNNGACUUAAGUCG
Entity 2
non-polymer
| 描述 description | ;[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]phosphinic acid
; |
| 分子量 formula_weight | 758.5 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 4 |
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 | 56 |
Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand.
Rsc Chem Biol (2023)
Files (7)
- pr_distribution /app/data/pr_computation/sy/8sy1/pr_distribution.json
- pr_output /app/data/pr_computation/sy/8sy1/8sy1.pr.out
- pr_plot /app/data/visualization/pr_computation/sy/8sy1/8sy1_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/sy/8sy1/8sy1.dat
- saxs_fit /app/data/saxs_computation/sy/8sy1/8sy1.fit
- saxs_log /app/data/saxs_computation/sy/8sy1/8sy1.log
- saxs_plot /app/data/visualization/saxs_computation/sy/8sy1/8sy1_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/sy/8sy1/8sy1.fit |
| pddf |
/app/data/pr_computation/sy/8sy1/8sy1.pr.out |
| profile |
/app/data/saxs_computation/sy/8sy1/8sy1.dat |