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 | 1i2x |
| 沉积日期 deposition_date | 2001-02-12 |
| 结构标题 title | 2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM |
| 关键词 keywords | ;'adenine bulge, A-type NA, DNA/RNA hybrid', DNA-RNA HYBRID
;; DNA-RNA HYBRID |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 19.31 Å |
| 回转半径 Rg (电子) rg_electron | 19.08 Å |
| 零角强度 I(0) i0 | 9528720.00 |
| 分子量 molecular_weight | 13998.0 kDa |
| 排除体积 excluded_volume | 13457 ų |
| 包络体积 envelope_volume | 21616 ų |
| 水化壳体积 shell_volume | 10668 ų |
| 包络直径 envelope_diameter | 65.3 Å |
| 壳层 Rg shell_rg | 23.22 Å |
| 包络 Rg envelope_rg | 18.84 Å |
| 形状 Rg shape_rg | 19.04 Å |
| 总 Rg total_rg | 19.61 Å |
| 总原子数 total_atoms | 930 |
| 残基数 n_residues | 44 |
| 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 | 65.5 Å |
| Rg (实空间) rg_real | 19.49 Å |
| Rg 误差 (实空间) rg_real_error | 0.48 Å |
| I(0) (实空间) i0_real | 9.5290e+06 |
| I(0) 误差 (实空间) i0_real_error | 1.2360e+05 |
| Rg (倒空间) rg_reciprocal | 19.46 Å |
| I(0) (倒空间) i0_reciprocal | 9529000.0000 |
| 解质量估计 total_estimate | 0.8604 |
| 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 | 18.4 Å |
| 偏度 Skewness skewness | 0.463 |
| 峰度 Kurtosis kurtosis | -0.369 |
| 角度范围 angular_range | — – 0.4100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 331400.0000 |
| 实空间数据点数 n_real_points | 72 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.858;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.711;
Smooth: 0.895
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 27.690 Å |
| 晶胞边长 b length_b | 47.710 Å |
| 晶胞边长 c length_c | 113.620 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 | 16 |
对称性 Symmetry
| 空间群 space_group | P 21 21 21 |
| 空间群编号 int_tables_number | 19 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 2.400 Å |
| 最低分辨率 resolution_low | 10.000 Å |
| R 因子 r_factor | — |
| R_work r_work | 0.2495 |
| R_free r_free | 0.2782 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
; |
| 分子量 formula_weight | 3471.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 4 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide/polyribonucleotide hybrid |
| 链编号 strand_id | A,B,D,C |
| 原子数 atom_count | 1009 |
GCGATATACGU
Entity 2
non-polymer
| 描述 description | SPERMIDINE |
| 分子量 formula_weight | 145.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
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 | 79 |
;X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
;
RNA (2001)
Files (7)
- pr_distribution /app/data/pr_computation/i2/1i2x/pr_distribution.json
- pr_output /app/data/pr_computation/i2/1i2x/1i2x.pr.out
- pr_plot /app/data/visualization/pr_computation/i2/1i2x/1i2x_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/i2/1i2x/1i2x.dat
- saxs_fit /app/data/saxs_computation/i2/1i2x/1i2x.fit
- saxs_log /app/data/saxs_computation/i2/1i2x/1i2x.log
- saxs_plot /app/data/visualization/saxs_computation/i2/1i2x/1i2x_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/i2/1i2x/1i2x.fit |
| pddf |
/app/data/pr_computation/i2/1i2x/1i2x.pr.out |
| profile |
/app/data/saxs_computation/i2/1i2x/1i2x.dat |