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 | 1fvm |
| 沉积日期 deposition_date | 2000-09-20 |
| 结构标题 title | Complex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA |
| 关键词 keywords | PEPTIDE-ANTIBIOTIC COMPLEX, GLYCOPEPTIDE, ANTIBIOTIC, VANCOMYCIN, CELL WALL PRECURSOR, STRUCTURAL PROTEIN-ANTIBIOTIC COMPLEX; PEPTIDE/ANTIBIOTIC |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 13.95 Å |
| 回转半径 Rg (电子) rg_electron | 13.09 Å |
| 零角强度 I(0) i0 | 2325630.00 |
| 分子量 molecular_weight | 11021.0 kDa |
| 排除体积 excluded_volume | 13866 ų |
| 包络体积 envelope_volume | 14510 ų |
| 水化壳体积 shell_volume | 9780 ų |
| 包络直径 envelope_diameter | 46.3 Å |
| 壳层 Rg shell_rg | 18.31 Å |
| 包络 Rg envelope_rg | 13.56 Å |
| 形状 Rg shape_rg | 13.02 Å |
| 总 Rg total_rg | 14.48 Å |
| 总原子数 total_atoms | 762 |
| 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 | 48.1 Å |
| Rg (实空间) rg_real | 13.91 Å |
| Rg 误差 (实空间) rg_real_error | 0.36 Å |
| I(0) (实空间) i0_real | 2.3260e+06 |
| I(0) 误差 (实空间) i0_real_error | 2.7670e+04 |
| Rg (倒空间) rg_reciprocal | 13.91 Å |
| I(0) (倒空间) i0_reciprocal | 2326000.0000 |
| 解质量估计 total_estimate | 0.7260 |
| 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 | 15.8 Å |
| 偏度 Skewness skewness | 0.269 |
| 峰度 Kurtosis kurtosis | -0.350 |
| 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 | 1209000.0000 |
| 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: 0.794;
Stabil: 1.000;
Sysdev: 0.368;
Positv: 1.000;
Valcen: 0.955;
Smooth: 0.993
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 35.637 Å |
| 晶胞边长 b length_b | 36.425 Å |
| 晶胞边长 c length_c | 65.728 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 | 24 |
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 | 1.800 Å |
| 最低分辨率 resolution_low | 5.000 Å |
| R 因子 r_factor | 0.1440 |
| R_work r_work | 0.1440 |
| R_free r_free | — |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | VANCOMYCIN |
| 分子量 formula_weight | 1150.0 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 6 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | A,B,C,D,E,F |
| 原子数 atom_count | 874 |
XXNGGYX
Entity 2
polymer
| 描述 description | DI-ACETYL-LYS-D-ALA-D-ALA |
| 分子量 formula_weight | 372.4 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 6 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | G,H,I,J,K,L |
KAA
Entity 3
branched
| 描述 description | vancosamine-(1-2)-beta-D-glucopyranose |
| 分子量 formula_weight | 323.3 kDa |
| 来源方法 src_method | man |
| 拷贝数 entity_count | 6 |
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 | 112 |
Crystal Structures of the Complexes between Vancomycin and Cell-Wall Precursor Analogs.
J.Mol.Biol. (2009)
Files (7)
- pr_distribution /app/data/pr_computation/fv/1fvm/pr_distribution.json
- pr_output /app/data/pr_computation/fv/1fvm/1fvm.pr.out
- pr_plot /app/data/visualization/pr_computation/fv/1fvm/1fvm_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/fv/1fvm/1fvm.dat
- saxs_fit /app/data/saxs_computation/fv/1fvm/1fvm.fit
- saxs_log /app/data/saxs_computation/fv/1fvm/1fvm.log
- saxs_plot /app/data/visualization/saxs_computation/fv/1fvm/1fvm_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/fv/1fvm/1fvm.fit |
| pddf |
/app/data/pr_computation/fv/1fvm/1fvm.pr.out |
| profile |
/app/data/saxs_computation/fv/1fvm/1fvm.dat |