SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
下载 Download
| 条目编号 entry_id | 8sjv |
| 沉积日期 deposition_date | 2023-04-18 |
| 结构标题 title | [4T24] Self-assembling left-handed tensegrity triangle with 24 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 | 23.89 Å |
| 回转半径 Rg (电子) rg_electron | 23.45 Å |
| 零角强度 I(0) i0 | 29961500.00 |
| 分子量 molecular_weight | 25415.0 kDa |
| 排除体积 excluded_volume | 24515 ų |
| 包络体积 envelope_volume | 41651 ų |
| 水化壳体积 shell_volume | 16251 ų |
| 包络直径 envelope_diameter | 78.4 Å |
| 壳层 Rg shell_rg | 28.02 Å |
| 包络 Rg envelope_rg | 23.33 Å |
| 形状 Rg shape_rg | 23.37 Å |
| 总 Rg total_rg | 23.99 Å |
| 总原子数 total_atoms | 1681 |
| 残基数 n_residues | 82 |
| 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 | 76.5 Å |
| Rg (实空间) rg_real | 23.87 Å |
| Rg 误差 (实空间) rg_real_error | 0.61 Å |
| I(0) (实空间) i0_real | 2.9960e+07 |
| I(0) 误差 (实空间) i0_real_error | 4.1960e+05 |
| Rg (倒空间) rg_reciprocal | 23.87 Å |
| I(0) (倒空间) i0_reciprocal | 29960000.0000 |
| 解质量估计 total_estimate | 0.9100 |
| 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 | 31.1 Å |
| 偏度 Skewness skewness | 0.190 |
| 峰度 Kurtosis kurtosis | -0.578 |
| 角度范围 angular_range | — – 0.3300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 1034000.0000 |
| 实空间数据点数 n_real_points | 65 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.959;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.954;
Smooth: 0.996
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 225.409 Å |
| 晶胞边长 b length_b | 225.409 Å |
| 晶胞边长 c length_c | 88.324 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 | 8.590 Å |
| 最低分辨率 resolution_low | 32.750 Å |
| R 因子 r_factor | 0.1825 |
| R_work r_work | 0.1795 |
| R_free r_free | 0.2803 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | ;DNA (5'-D(P*GP*AP*CP*AP*TP*CP*AP*CP*AP*GP*TP*GP*GP*AP*CP*TP*AP*CP*AP*AP*G)-3')
; |
| 分子量 formula_weight | 6465.2 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 | A |
| 原子数 atom_count | 1681 |
GACATCACAGTGGACTACAAG
Entity 2
polymer
| 描述 description | ;DNA (5'-D(P*TP*CP*CP*TP*TP*GP*TP*AP*GP*TP*GP*GP*AP*GP*TP*GP*T)-3')
; |
| 分子量 formula_weight | 5264.4 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 | B |
TCCTTGTAGTGGAGTGT
Entity 3
polymer
| 描述 description | ;DNA (5'-D(P*GP*AP*AP*CP*AP*CP*TP*CP*CP*TP*GP*AP*GP*AP*CP*TP*AP*CP*AP*A)-3')
; |
| 分子量 formula_weight | 6096.0 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 |
GAACACTCCTGAGACTACAA
Entity 4
polymer
| 描述 description | ;DNA (5'-D(P*CP*TP*TP*GP*TP*AP*GP*TP*CP*TP*CP*AP*CP*CP*AP*CP*TP*GP*TP*GP*AP*TP*GP*T)-3')
; |
| 分子量 formula_weight | 7326.7 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polydeoxyribonucleotide |
| 链编号 strand_id | D |
CTTGTAGTCTCACCACTGTGATGT
Engineering tertiary chirality in helical biopolymers.
Proc.Natl.Acad.Sci.USA (2024)
Files (7)
- pr_distribution /app/data/pr_computation/sj/8sjv/pr_distribution.json
- pr_output /app/data/pr_computation/sj/8sjv/8sjv.pr.out
- pr_plot /app/data/visualization/pr_computation/sj/8sjv/8sjv_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/sj/8sjv/8sjv.dat
- saxs_fit /app/data/saxs_computation/sj/8sjv/8sjv.fit
- saxs_log /app/data/saxs_computation/sj/8sjv/8sjv.log
- saxs_plot /app/data/visualization/saxs_computation/sj/8sjv/8sjv_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/sj/8sjv/8sjv.fit |
| pddf |
/app/data/pr_computation/sj/8sjv/8sjv.pr.out |
| profile |
/app/data/saxs_computation/sj/8sjv/8sjv.dat |