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 | 8qww |
| 沉积日期 deposition_date | 2023-10-20 |
| 结构标题 title | Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 10% ethanol without TFA |
| 关键词 keywords | amyloid, PROTEIN FIBRIL; PROTEIN FIBRIL |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 10.81 Å |
| 回转半径 Rg (电子) rg_electron | 10.30 Å |
| 零角强度 I(0) i0 | 70907.70 |
| 分子量 molecular_weight | 1670.0 kDa |
| 排除体积 excluded_volume | 2261 ų |
| 包络体积 envelope_volume | 2880 ų |
| 水化壳体积 shell_volume | 3187 ų |
| 包络直径 envelope_diameter | 35.8 Å |
| 壳层 Rg shell_rg | 13.08 Å |
| 包络 Rg envelope_rg | 10.73 Å |
| 形状 Rg shape_rg | 10.29 Å |
| 总 Rg total_rg | 11.73 Å |
| 总原子数 total_atoms | 243 |
| 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 | 41.1 Å |
| Rg (实空间) rg_real | 11.05 Å |
| Rg 误差 (实空间) rg_real_error | 0.58 Å |
| I(0) (实空间) i0_real | 7.0910e+04 |
| I(0) 误差 (实空间) i0_real_error | 9.7500e+02 |
| Rg (倒空间) rg_reciprocal | 11.03 Å |
| I(0) (倒空间) i0_reciprocal | 70910.0000 |
| 解质量估计 total_estimate | 0.7712 |
| 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 | 10.4 Å |
| 偏度 Skewness skewness | 0.681 |
| 峰度 Kurtosis kurtosis | 0.101 |
| 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 | 10160.0000 |
| 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: 0.601;
Stabil: 0.999;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.227;
Smooth: 0.995
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 4.874 Å |
| 晶胞边长 b length_b | 42.270 Å |
| 晶胞边长 c length_c | 21.442 Å |
| 晶胞夹角 α angle_alpha | 90.00 ° |
| 晶胞夹角 β angle_beta | 95.62 ° |
| 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 1 21 1 |
| 空间群编号 int_tables_number | 4 |
| 晶系 crystal_system | monoclinic |
精修参数 Refinement
| 分辨率 resolution | 1.500 Å |
| 最低分辨率 resolution_low | 19.050 Å |
| R 因子 r_factor | 0.1396 |
| R_work r_work | 0.1357 |
| R_free r_free | 0.1737 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | Peptide LYIQWL from Tc5b |
| 分子量 formula_weight | 835.0 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | A,B |
| 原子数 atom_count | 284 |
LYIQWL
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 | 1 |
Solvent induced amyloid polymorphism and the uncovering of the elusive class 3 amyloid topology.
Commun Biol (2024)
Files (7)
- pr_distribution /app/data/pr_computation/qw/8qww/pr_distribution.json
- pr_output /app/data/pr_computation/qw/8qww/8qww.pr.out
- pr_plot /app/data/visualization/pr_computation/qw/8qww/8qww_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/qw/8qww/8qww.dat
- saxs_fit /app/data/saxs_computation/qw/8qww/8qww.fit
- saxs_log /app/data/saxs_computation/qw/8qww/8qww.log
- saxs_plot /app/data/visualization/saxs_computation/qw/8qww/8qww_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/qw/8qww/8qww.fit |
| pddf |
/app/data/pr_computation/qw/8qww/8qww.pr.out |
| profile |
/app/data/saxs_computation/qw/8qww/8qww.dat |