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 | 9kbr |
| 沉积日期 deposition_date | 2024-10-31 |
| 结构标题 title | Crystal structure of the methyltransferase-ribozyme 1 bound to DNA substrate (with 1-methyl-adenosine) |
| 关键词 keywords | Ribozyme, Methyltransferase, MTR1, O6-methylguanine, DNA-RNA HYBRID; DNA-RNA HYBRID |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 19.16 Å |
| 回转半径 Rg (电子) rg_electron | 18.96 Å |
| 零角强度 I(0) i0 | 19231900.00 |
| 分子量 molecular_weight | 19902.0 kDa |
| 排除体积 excluded_volume | 18902 ų |
| 包络体积 envelope_volume | 27631 ų |
| 水化壳体积 shell_volume | 13602 ų |
| 包络直径 envelope_diameter | 66.0 Å |
| 壳层 Rg shell_rg | 23.05 Å |
| 包络 Rg envelope_rg | 18.93 Å |
| 形状 Rg shape_rg | 18.90 Å |
| 总 Rg total_rg | 19.45 Å |
| 总原子数 total_atoms | 1316 |
| 残基数 n_residues | 61 |
| 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 | 64.4 Å |
| Rg (实空间) rg_real | 19.20 Å |
| Rg 误差 (实空间) rg_real_error | 0.53 Å |
| I(0) (实空间) i0_real | 1.9230e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.5070e+05 |
| Rg (倒空间) rg_reciprocal | 19.20 Å |
| I(0) (倒空间) i0_reciprocal | 19230000.0000 |
| 解质量估计 total_estimate | 0.7977 |
| 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 | 17.0 Å |
| 偏度 Skewness skewness | 0.363 |
| 峰度 Kurtosis kurtosis | -0.371 |
| 角度范围 angular_range | — – 0.4150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2118000.0000 |
| 实空间数据点数 n_real_points | 73 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.827;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.884;
Smooth: 0.000
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 69.196 Å |
| 晶胞边长 b length_b | 69.196 Å |
| 晶胞边长 c length_c | 65.597 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 | 4 |
对称性 Symmetry
| 空间群 space_group | P 41 |
| 空间群编号 int_tables_number | 76 |
| 晶系 crystal_system | tetragonal |
精修参数 Refinement
| 分辨率 resolution | 2.650 Å |
| 最低分辨率 resolution_low | 34.600 Å |
| R 因子 r_factor | 0.1905 |
| R_work r_work | 0.1887 |
| R_free r_free | 0.2231 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA (5'-D(*CP*CP*AP*CP*TP*GP*(MA7)P*GP*AP*GP*CP*TP*TP*C)-3')
; |
| 分子量 formula_weight | 4255.8 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | A |
| 原子数 atom_count | 1317 |
CCACTGAGAGCTTC
Entity 2
polymer
| 描述 description | ;RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')
; |
| 分子量 formula_weight | 7641.6 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polyribonucleotide |
| 链编号 strand_id | B |
GGAAGCUCUGACCGACCCCCAGCC
Entity 3
polymer
| 描述 description | ;RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')
; |
| 分子量 formula_weight | 7755.7 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polyribonucleotide |
| 链编号 strand_id | C |
GCUGGGACAACUAGACAUACAGUG
Entity 4
non-polymer
| 描述 description | SODIUM ION |
| 分子量 formula_weight | 23.0 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 4 |
Entity 5
non-polymer
| 描述 description | GUANINE |
| 分子量 formula_weight | 151.1 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
Entity 6
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 | 1 |
Site-specific ribozyme-mediated alkylation of DNA substrates.
Nucleic Acids Res. (2026)
Files (7)
- pr_distribution /app/data/pr_computation/kb/9kbr/pr_distribution.json
- pr_output /app/data/pr_computation/kb/9kbr/9kbr.pr.out
- pr_plot /app/data/visualization/pr_computation/kb/9kbr/9kbr_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/kb/9kbr/9kbr.dat
- saxs_fit /app/data/saxs_computation/kb/9kbr/9kbr.fit
- saxs_log /app/data/saxs_computation/kb/9kbr/9kbr.log
- saxs_plot /app/data/visualization/saxs_computation/kb/9kbr/9kbr_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/kb/9kbr/9kbr.fit |
| pddf |
/app/data/pr_computation/kb/9kbr/9kbr.pr.out |
| profile |
/app/data/saxs_computation/kb/9kbr/9kbr.dat |