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 | 8sjq |
| 沉积日期 deposition_date | 2023-04-18 |
| 结构标题 title | [3T16] Self-assembling right-handed tensegrity triangle with 16 interjunction base pairs and R3 symmetry |
| 关键词 keywords | Tensegrity triangle, DNA nanotechnology, nanomaterials, DNA; DNA |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 19.98 Å |
| 回转半径 Rg (电子) rg_electron | 19.54 Å |
| 零角强度 I(0) i0 | 17428700.00 |
| 分子量 molecular_weight | 19093.0 kDa |
| 排除体积 excluded_volume | 18389 ų |
| 包络体积 envelope_volume | 29410 ų |
| 水化壳体积 shell_volume | 13870 ų |
| 包络直径 envelope_diameter | 66.2 Å |
| 壳层 Rg shell_rg | 23.64 Å |
| 包络 Rg envelope_rg | 19.29 Å |
| 形状 Rg shape_rg | 19.45 Å |
| 总 Rg total_rg | 20.09 Å |
| 总原子数 total_atoms | 1265 |
| 残基数 n_residues | 62 |
| 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 | 64.9 Å |
| Rg (实空间) rg_real | 19.94 Å |
| Rg 误差 (实空间) rg_real_error | 0.40 Å |
| I(0) (实空间) i0_real | 1.7430e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.1920e+05 |
| Rg (倒空间) rg_reciprocal | 19.95 Å |
| I(0) (倒空间) i0_reciprocal | 17430000.0000 |
| 解质量估计 total_estimate | 0.9002 |
| 解质量评级 solution_quality |
EXCELLENT
a EXCELLENT solution
|
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 28.4 Å |
| 偏度 Skewness skewness | 0.199 |
| 峰度 Kurtosis kurtosis | -0.452 |
| 角度范围 angular_range | — – 0.4000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 983800.0000 |
| 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: 0.911;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.972;
Smooth: 0.993
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 167.658 Å |
| 晶胞边长 b length_b | 167.658 Å |
| 晶胞边长 c length_c | 91.904 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 | 9 |
对称性 Symmetry
| 空间群 space_group | H 3 |
| 空间群编号 int_tables_number | 146 |
| 晶系 crystal_system | trigonal |
精修参数 Refinement
| 分辨率 resolution | 6.190 Å |
| 最低分辨率 resolution_low | 35.230 Å |
| R 因子 r_factor | 0.1107 |
| R_work r_work | 0.1087 |
| R_free r_free | 0.1374 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA (5'-D(*CP*AP*GP*CP*AP*TP*GP*CP*CP*TP*GP*AP*TP*AP*CP*CP*GP*CP*A)-3')
; |
| 分子量 formula_weight | 5774.8 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 | 1265 |
CAGCATGCCTGATACCGCA
Entity 2
polymer
| 描述 description | ;DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')
; |
| 分子量 formula_weight | 4883.2 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 | B |
TGCGGTATCACCACGA
Entity 3
polymer
| 描述 description | ;DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*AP*TP*GP*C)-3')
; |
| 分子量 formula_weight | 4617.0 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 | C |
TGCGCTGTGGCATGC
Entity 4
polymer
| 描述 description | ;DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')
; |
| 分子量 formula_weight | 3703.4 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 | D |
TCGTGGACAGCG
Engineering tertiary chirality in helical biopolymers.
Proc.Natl.Acad.Sci.USA (2024)
Files (7)
- pr_distribution /app/data/pr_computation/sj/8sjq/pr_distribution.json
- pr_output /app/data/pr_computation/sj/8sjq/8sjq.pr.out
- pr_plot /app/data/visualization/pr_computation/sj/8sjq/8sjq_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/sj/8sjq/8sjq.dat
- saxs_fit /app/data/saxs_computation/sj/8sjq/8sjq.fit
- saxs_log /app/data/saxs_computation/sj/8sjq/8sjq.log
- saxs_plot /app/data/visualization/saxs_computation/sj/8sjq/8sjq_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/sj/8sjq/8sjq.fit |
| pddf |
/app/data/pr_computation/sj/8sjq/8sjq.pr.out |
| profile |
/app/data/saxs_computation/sj/8sjq/8sjq.dat |