ソフトウェア | 名称 | バージョン | 分類 |
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BUSTER | 2.11.7精密化 | PDB_EXTRACT | 3.25 | データ抽出 | XDS | | データ削減 | Aimless | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5VB9 解像度: 2.17→79.1 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.173 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.15
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.227 | 2362 | 5.03 % | RANDOM |
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Rwork | 0.208 | - | - | - |
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obs | 0.209 | 46955 | 100 % | - |
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原子変位パラメータ | Biso max: 233.06 Å2 / Biso mean: 69.14 Å2 / Biso min: 38.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.3586 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.3586 Å2 | 0 Å2 |
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3- | - | - | -0.7173 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.29 Å |
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精密化ステップ | サイクル: final / 解像度: 2.17→79.1 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4185 | 0 | 0 | 163 | 4348 |
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Biso mean | - | - | - | 61.71 | - |
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残基数 | - | - | - | - | 545 |
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拘束条件 | Refine-ID | タイプ | 数 | Restraint function | Weight | Dev ideal |
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X-RAY DIFFRACTION | t_dihedral_angle_d1408 | SINUSOIDAL2 | | X-RAY DIFFRACTION | t_trig_c_planes | | | | X-RAY DIFFRACTION | t_gen_planes723 | HARMONIC5 | | X-RAY DIFFRACTION | t_it4298 | HARMONIC20 | | X-RAY DIFFRACTION | t_nbd | | | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion560 | SEMIHARMONIC5 | | X-RAY DIFFRACTION | t_sum_occupancies | | | | X-RAY DIFFRACTION | t_utility_distance | | | | X-RAY DIFFRACTION | t_utility_angle | | | | X-RAY DIFFRACTION | t_utility_torsion | | | | X-RAY DIFFRACTION | t_ideal_dist_contact4636 | SEMIHARMONIC4 | | X-RAY DIFFRACTION | t_bond_d4298 | HARMONIC2 | 0.008 | X-RAY DIFFRACTION | t_angle_deg5860 | HARMONIC2 | 1.08 | X-RAY DIFFRACTION | t_omega_torsion | | | 3.48 | X-RAY DIFFRACTION | t_other_torsion | | | 17.59 | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.17→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2457 | 42 | 4.47 % |
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Rwork | 0.2136 | 898 | - |
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all | 0.2149 | 940 | - |
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obs | - | - | 100 % |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 5.0101 | -0.6122 | -1.0845 | 2.0732 | -0.4593 | 2.5725 | 0.3029 | -0.1017 | 0.2925 | 0.1692 | 0.0009 | -0.1246 | -0.6164 | 0.3705 | -0.3038 | 0.205 | -0.1083 | 0.0937 | -0.2046 | -0.0583 | -0.1646 | 50.999 | -8.9056 | 22.0292 | 2 | 2.1139 | 0.5913 | -1.4453 | 4.258 | -0.5225 | 2.8787 | 0.1166 | -0.1101 | 0.035 | 0.2886 | -0.1237 | 0.0072 | 0.0737 | 0.0321 | 0.007 | 0.2333 | 0.0069 | 0.1113 | -0.1756 | 0.0429 | 0.0645 | 22.2612 | -19.5271 | 41.7225 | 3 | 2.4988 | 0.1029 | -1.0448 | 3.2475 | -1.5479 | 3.0455 | -0.1363 | -0.2394 | -0.4151 | 0.198 | 0.0976 | 0.074 | 0.0868 | 0.4623 | 0.0387 | 0.0784 | 0.0347 | 0.0232 | -0.0777 | 0.0008 | -0.0376 | 52.7272 | -30.8878 | 24.2803 | 4 | 3.8004 | -0.1691 | -0.7127 | 2.5061 | -0.1121 | 1.5958 | -0.0876 | 0.1166 | -0.1817 | -0.2302 | -0.039 | 0.2431 | 0.0815 | -0.2117 | 0.1266 | 0.1908 | 0.0199 | 0.1011 | -0.2305 | 0.0159 | 0.0304 | 17.5902 | -32.0323 | 33.1459 | 5 | 3.3779 | -0.2499 | 0.1969 | 1.5881 | 0.1688 | 4.3756 | 0.0448 | 0.3791 | 0.864 | -0.1746 | 0.1058 | -0.4778 | -1.0313 | 0.7145 | -0.1506 | 0.3328 | -0.304 | 0.1546 | 0.09 | -0.0188 | 0.1242 | 68.762 | 1.9817 | 0.2148 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | { A|1 - A|126 } | A1 - 126 | 2 | X-RAY DIFFRACTION | 2 | { A|127 - A|230 } | A127 - 230 | 3 | X-RAY DIFFRACTION | 3 | { B|1 - B|108 } | B1 - 108 | 4 | X-RAY DIFFRACTION | 4 | { B|109 - B|213 } | B109 - 213 | 5 | X-RAY DIFFRACTION | 5 | { C|60 - C|161 } | C60 - 161 | | | | | |
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