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 | 1ob7 |
| 沉积日期 deposition_date | 2003-01-24 |
| 结构标题 title | Cephaibol C |
| 关键词 keywords | ION CHANNEL, CEPHAIBOL, PEPTAIBOL, ANTIBACTERIAL, ANTIFUNGAL, ANTIBIOTIC; ANTIBIOTIC |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 9.77 Å |
| 回转半径 Rg (电子) rg_electron | 9.05 Å |
| 零角强度 I(0) i0 | 70900.70 |
| 分子量 molecular_weight | 1784.0 kDa |
| 排除体积 excluded_volume | 2460 ų |
| 包络体积 envelope_volume | 2662 ų |
| 水化壳体积 shell_volume | 3174 ų |
| 包络直径 envelope_diameter | 31.7 Å |
| 壳层 Rg shell_rg | 12.59 Å |
| 包络 Rg envelope_rg | 9.58 Å |
| 形状 Rg shape_rg | 9.02 Å |
| 总 Rg total_rg | 10.90 Å |
| 总原子数 total_atoms | 125 |
| 残基数 n_residues | 5 |
| 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 | 35.9 Å |
| Rg (实空间) rg_real | 9.96 Å |
| Rg 误差 (实空间) rg_real_error | 0.54 Å |
| I(0) (实空间) i0_real | 7.0900e+04 |
| I(0) 误差 (实空间) i0_real_error | 8.5960e+02 |
| Rg (倒空间) rg_reciprocal | 9.95 Å |
| I(0) (倒空间) i0_reciprocal | 70900.0000 |
| 解质量估计 total_estimate | 0.7832 |
| 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 | 9.1 Å |
| 偏度 Skewness skewness | 0.558 |
| 峰度 Kurtosis kurtosis | -0.273 |
| 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 | 3844.0000 |
| 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: 0.666;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.215;
Smooth: 0.965
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 9.002 Å |
| 晶胞边长 b length_b | 28.619 Å |
| 晶胞边长 c length_c | 41.100 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 | 4 |
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 | 0.890 Å |
| 最低分辨率 resolution_low | 28.620 Å |
| R 因子 r_factor | 0.0716 |
| R_work r_work | — |
| R_free r_free | 0.0770 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | CEPHAIBOL C |
| 分子量 formula_weight | 1655.0 kDa |
| 来源方法 src_method | nat |
| 拷贝数 entity_count | 1 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | A |
| 原子数 atom_count | 146 |
XFAAAAGLVAPQVPAPF
Entity 2
non-polymer
| 描述 description | ETHANOL |
| 分子量 formula_weight | 46.1 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 2 |
Entity 3
non-polymer
| 描述 description | SODIUM ION |
| 分子量 formula_weight | 23.0 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 1 |
Entity 4
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 | 11 |
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d1ob7a_ |
| 类 Class class | j — Peptides |
| 折叠类型 Fold fold | j.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids |
| 超家族 Superfamily superfamily | j.1.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids |
| 家族 Family family | j.1.1.2 — Peptaibol |
Crystal Structures of Cephaibols
J.Pept.Sci. (2003)
Files (7)
- pr_distribution /app/data/pr_computation/ob/1ob7/pr_distribution.json
- pr_output /app/data/pr_computation/ob/1ob7/1ob7.pr.out
- pr_plot /app/data/visualization/pr_computation/ob/1ob7/1ob7_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/ob/1ob7/1ob7.dat
- saxs_fit /app/data/saxs_computation/ob/1ob7/1ob7.fit
- saxs_log /app/data/saxs_computation/ob/1ob7/1ob7.log
- saxs_plot /app/data/visualization/saxs_computation/ob/1ob7/1ob7_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/ob/1ob7/1ob7.fit |
| pddf |
/app/data/pr_computation/ob/1ob7/1ob7.pr.out |
| profile |
/app/data/saxs_computation/ob/1ob7/1ob7.dat |