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 | 1m6r |
| 沉积日期 deposition_date | 2002-07-17 |
| 结构标题 title | ;Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang
; |
| 关键词 keywords | Z-DNA, overhang, DNA; DNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 9.51 Å |
| 回转半径 Rg (电子) rg_electron | 8.73 Å |
| 零角强度 I(0) i0 | 760778.00 |
| 分子量 molecular_weight | 3594.0 kDa |
| 排除体积 excluded_volume | 3467 ų |
| 包络体积 envelope_volume | 4249 ų |
| 水化壳体积 shell_volume | 4703 ų |
| 包络直径 envelope_diameter | 29.0 Å |
| 壳层 Rg shell_rg | 13.03 Å |
| 包络 Rg envelope_rg | 8.94 Å |
| 形状 Rg shape_rg | 8.69 Å |
| 总 Rg total_rg | 9.73 Å |
| 总原子数 total_atoms | 240 |
| 残基数 n_residues | 12 |
| 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 | 32.0 Å |
| Rg (实空间) rg_real | 9.48 Å |
| Rg 误差 (实空间) rg_real_error | 0.27 Å |
| I(0) (实空间) i0_real | 7.6080e+05 |
| I(0) 误差 (实空间) i0_real_error | 7.5700e+03 |
| Rg (倒空间) rg_reciprocal | 9.48 Å |
| I(0) (倒空间) i0_reciprocal | 760800.0000 |
| 解质量估计 total_estimate | 0.8856 |
| 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 | 11.7 Å |
| 偏度 Skewness skewness | 0.228 |
| 峰度 Kurtosis kurtosis | -0.270 |
| 角度范围 angular_range | — – 0.5000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 42440.0000 |
| 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: 0.844;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.989;
Smooth: 0.989
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 17.960 Å |
| 晶胞边长 b length_b | 31.470 Å |
| 晶胞边长 c length_c | 44.730 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 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 | 1.540 Å |
| 最低分辨率 resolution_low | 8.000 Å |
| R 因子 r_factor | — |
| R_work r_work | 0.1620 |
| R_free r_free | 0.1910 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | 5'-R(*G)D(*CP*GP*CP*GP*CP*G)-3' |
| 分子量 formula_weight | 2139.4 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | A,B |
| 原子数 atom_count | 303 |
GCGCGCG
Entity 2
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 |
;Crystal structure of rGd(CGCGCG): a Z-DNA hexamer duplex with a 5'-(rG) overhang.
;
Acta Crystallogr.,Sect.D (2003)
Files (7)
- pr_distribution /app/data/pr_computation/m6/1m6r/pr_distribution.json
- pr_output /app/data/pr_computation/m6/1m6r/1m6r.pr.out
- pr_plot /app/data/visualization/pr_computation/m6/1m6r/1m6r_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/m6/1m6r/1m6r.dat
- saxs_fit /app/data/saxs_computation/m6/1m6r/1m6r.fit
- saxs_log /app/data/saxs_computation/m6/1m6r/1m6r.log
- saxs_plot /app/data/visualization/saxs_computation/m6/1m6r/1m6r_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/m6/1m6r/1m6r.fit |
| pddf |
/app/data/pr_computation/m6/1m6r/1m6r.pr.out |
| profile |
/app/data/saxs_computation/m6/1m6r/1m6r.dat |