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 | 8t84 |
| 沉积日期 deposition_date | 2023-06-21 |
| 结构标题 title | Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms heterochiral rippled beta-sheet, includes hexafluoroisopropanol |
| 关键词 keywords | Rippled beta sheet, amyloid fibril, PROTEIN FIBRIL; PROTEIN FIBRIL |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 8.29 Å |
| 回转半径 Rg (电子) rg_electron | 7.37 Å |
| 零角强度 I(0) i0 | 45535.90 |
| 分子量 molecular_weight | 896.8 kDa |
| 排除体积 excluded_volume | 1019 ų |
| 包络体积 envelope_volume | 1319 ų |
| 水化壳体积 shell_volume | 2182 ų |
| 包络直径 envelope_diameter | 26.0 Å |
| 壳层 Rg shell_rg | 10.27 Å |
| 包络 Rg envelope_rg | 7.70 Å |
| 形状 Rg shape_rg | 7.27 Å |
| 总 Rg total_rg | 8.81 Å |
| 总原子数 total_atoms | 106 |
| 残基数 n_residues | 6 |
| 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 | 30.3 Å |
| Rg (实空间) rg_real | 8.44 Å |
| Rg 误差 (实空间) rg_real_error | 0.35 Å |
| I(0) (实空间) i0_real | 4.5540e+04 |
| I(0) 误差 (实空间) i0_real_error | 4.7340e+02 |
| Rg (倒空间) rg_reciprocal | 8.43 Å |
| I(0) (倒空间) i0_reciprocal | 45540.0000 |
| 解质量估计 total_estimate | 0.7335 |
| 解质量评级 solution_quality |
REASONABLE
a REASONABLE solution
|
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 9.2 Å |
| 偏度 Skewness skewness | 0.613 |
| 峰度 Kurtosis kurtosis | 0.013 |
| 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 | 2995.0000 |
| 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: 0.555;
Stabil: 0.992;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.533;
Smooth: 0.358
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 9.420 Å |
| 晶胞边长 b length_b | 11.220 Å |
| 晶胞边长 c length_c | 21.120 Å |
| 晶胞夹角 α angle_alpha | 96.56 ° |
| 晶胞夹角 β angle_beta | 89.57 ° |
| 晶胞夹角 γ angle_gamma | 94.95 ° |
| 晶胞分子数 Z z_pdb | 2 |
对称性 Symmetry
| 空间群 space_group | P -1 |
| 空间群编号 int_tables_number | 2 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 1.101 Å |
| 最低分辨率 resolution_low | 20.981 Å |
| R 因子 r_factor | — |
| R_work r_work | 0.1889 |
| R_free r_free | 0.2038 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | Racemic mixture of amyloid beta segment 35-MVGGVV-40 |
| 分子量 formula_weight | 560.7 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | AAA |
| 原子数 atom_count | 133 |
MVGGVV
Entity 2
non-polymer
| 描述 description | 1,1,1,3,3,3-hexafluoropropan-2-ol |
| 分子量 formula_weight | 168.0 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
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 | 2 |
Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets.
J.Am.Chem.Soc. (2023)
Files (7)
- pr_distribution /app/data/pr_computation/t8/8t84/pr_distribution.json
- pr_output /app/data/pr_computation/t8/8t84/8t84.pr.out
- pr_plot /app/data/visualization/pr_computation/t8/8t84/8t84_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/t8/8t84/8t84.dat
- saxs_fit /app/data/saxs_computation/t8/8t84/8t84.fit
- saxs_log /app/data/saxs_computation/t8/8t84/8t84.log
- saxs_plot /app/data/visualization/saxs_computation/t8/8t84/8t84_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/t8/8t84/8t84.fit |
| pddf |
/app/data/pr_computation/t8/8t84/8t84.pr.out |
| profile |
/app/data/saxs_computation/t8/8t84/8t84.dat |