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 | 1q7d |
| 沉积日期 deposition_date | 2003-08-18 |
| 结构标题 title | Structure of the integrin alpha2beta1 binding collagen peptide |
| 关键词 keywords | COLLAGEN, INTEGRIN, TRIPLEHELIX, CONTRACTILE PROTEIN; CONTRACTILE PROTEIN |
| 实验方法 method | X-RAY DIFFRACTION |
| 回转半径 Rg (Guinier) rg_guinier | 16.96 Å |
| 回转半径 Rg (电子) rg_electron | 17.82 Å |
| 零角强度 I(0) i0 | 873377.00 |
| 分子量 molecular_weight | 6057.0 kDa |
| 排除体积 excluded_volume | 7460 ų |
| 包络体积 envelope_volume | 9169 ų |
| 水化壳体积 shell_volume | 5934 ų |
| 包络直径 envelope_diameter | 66.8 Å |
| 壳层 Rg shell_rg | 18.76 Å |
| 包络 Rg envelope_rg | 18.33 Å |
| 形状 Rg shape_rg | 17.77 Å |
| 总 Rg total_rg | 18.18 Å |
| 总原子数 total_atoms | 429 |
| 残基数 n_residues | 45 |
| 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 | 44.9 Å |
| Rg (实空间) rg_real | 15.31 Å |
| Rg 误差 (实空间) rg_real_error | 0.12 Å |
| I(0) (实空间) i0_real | 8.2690e+05 |
| I(0) 误差 (实空间) i0_real_error | 8.3810e+03 |
| Rg (倒空间) rg_reciprocal | 17.44 Å |
| I(0) (倒空间) i0_reciprocal | 873300.0000 |
| 解质量估计 total_estimate | 0.6047 |
| 解质量评级 solution_quality |
REASONABLE
a REASONABLE solution
|
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 10.6 Å |
| 偏度 Skewness skewness | 0.408 |
| 峰度 Kurtosis kurtosis | -0.778 |
| 角度范围 angular_range | — – 0.4700 Å−1 |
| 当前正则化参数 α current_alpha | 2.8760 |
| 最高正则化参数 α highest_alpha | 37680.0000 |
| 实空间数据点数 n_real_points | 77 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.010;
Oscil: 0.891;
Stabil: 0.985;
Sysdev: 0.000;
Positv: 1.000;
Valcen: 0.333;
Smooth: 0.000
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 29.600 Å |
| 晶胞边长 b length_b | 135.800 Å |
| 晶胞边长 c length_c | 25.400 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 | C 2 2 21 |
| 空间群编号 int_tables_number | 20 |
| 晶系 crystal_system | — |
精修参数 Refinement
| 分辨率 resolution | 1.800 Å |
| 最低分辨率 resolution_low | 6.000 Å |
| R 因子 r_factor | 0.2363 |
| R_work r_work | 0.2363 |
| R_free r_free | 0.2660 |
衍射实验 Diffraction
Entity 1
polymer
| 描述 description | collagen alfa 1(I) chain peptide GPOGPOGFOGERGPOGPOGPO |
| 分子量 formula_weight | 2039.2 kDa |
| 来源方法 src_method | syn |
| 拷贝数 entity_count | 3 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | A,B,C |
| 原子数 atom_count | 523 |
XGPPGPPGFPGERGPPGPPGPPX
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 | 94 |
SCOP 2.08 (9 domains)
| 结构域编号 domain_id | d1q7da1 |
| 类 Class class | k — Designed proteins |
| 折叠类型 Fold fold | k.3 — Collagen-like peptides |
| 超家族 Superfamily superfamily | k.3.1 — Collagen-like peptides |
| 家族 Family family | k.3.1.1 — Collagen-like peptides |
| 结构域编号 domain_id | d1q7da2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1q7da3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1q7db1 |
| 类 Class class | k — Designed proteins |
| 折叠类型 Fold fold | k.3 — Collagen-like peptides |
| 超家族 Superfamily superfamily | k.3.1 — Collagen-like peptides |
| 家族 Family family | k.3.1.1 — Collagen-like peptides |
| 结构域编号 domain_id | d1q7db2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1q7db3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1q7dc1 |
| 类 Class class | k — Designed proteins |
| 折叠类型 Fold fold | k.3 — Collagen-like peptides |
| 超家族 Superfamily superfamily | k.3.1 — Collagen-like peptides |
| 家族 Family family | k.3.1.1 — Collagen-like peptides |
| 结构域编号 domain_id | d1q7dc2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1q7dc3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
Structure of the Integrin alpha2beta1-binding Collagen Peptide.
J.Mol.Biol. (2004)
Files (7)
- pr_distribution /app/data/pr_computation/q7/1q7d/pr_distribution.json
- pr_output /app/data/pr_computation/q7/1q7d/1q7d.pr.out
- pr_plot /app/data/visualization/pr_computation/q7/1q7d/1q7d_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/q7/1q7d/1q7d.dat
- saxs_fit /app/data/saxs_computation/q7/1q7d/1q7d.fit
- saxs_log /app/data/saxs_computation/q7/1q7d/1q7d.log
- saxs_plot /app/data/visualization/saxs_computation/q7/1q7d/1q7d_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/q7/1q7d/1q7d.fit |
| pddf |
/app/data/pr_computation/q7/1q7d/1q7d.pr.out |
| profile |
/app/data/saxs_computation/q7/1q7d/1q7d.dat |