ソフトウェア | 名称 | バージョン | 分類 |
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PHASER | | 位相決定 | PHENIX | (phenix.refine: 1.6.4_486)精密化 | XDS | (VERSION May 10データ削減 | SCALA | | データスケーリング | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 1GKU 解像度: 2.35→44.358 Å / SU ML: 0.38 / σ(F): 0 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2511 | 1955 | 5.07 % |
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Rwork | 0.2084 | - | - |
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obs | 0.2105 | 38558 | 90.43 % |
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溶媒の処理 | 減衰半径: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 44.82 Å2 / ksol: 0.296 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.2688 Å2 | -0 Å2 | 0 Å2 |
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2- | - | -4.9468 Å2 | 0 Å2 |
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3- | - | - | 5.2156 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.35→44.358 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6633 | 0 | 10 | 99 | 6742 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.012 | 6772 | X-RAY DIFFRACTION | f_angle_d1.564 | 9093 | X-RAY DIFFRACTION | f_dihedral_angle_d17.218 | 2582 | X-RAY DIFFRACTION | f_chiral_restr0.113 | 994 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1143 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.35-2.4088 | 0.4151 | 127 | 0.3937 | 2083 | X-RAY DIFFRACTION | 74 | 2.4088-2.4739 | 0.3947 | 114 | 0.3573 | 2232 | X-RAY DIFFRACTION | 78 | 2.4739-2.5467 | 0.4489 | 123 | 0.3428 | 2308 | X-RAY DIFFRACTION | 81 | 2.5467-2.6289 | 0.4178 | 135 | 0.332 | 2407 | X-RAY DIFFRACTION | 84 | 2.6289-2.7229 | 0.3864 | 127 | 0.319 | 2379 | X-RAY DIFFRACTION | 83 | 2.7229-2.8319 | 0.3275 | 141 | 0.2909 | 2514 | X-RAY DIFFRACTION | 88 | 2.8319-2.9607 | 0.3329 | 130 | 0.2678 | 2662 | X-RAY DIFFRACTION | 93 | 2.9607-3.1168 | 0.3132 | 155 | 0.2438 | 2764 | X-RAY DIFFRACTION | 97 | 3.1168-3.312 | 0.3201 | 156 | 0.2385 | 2812 | X-RAY DIFFRACTION | 97 | 3.312-3.5676 | 0.2493 | 153 | 0.2168 | 2815 | X-RAY DIFFRACTION | 98 | 3.5676-3.9265 | 0.2416 | 147 | 0.2119 | 2750 | X-RAY DIFFRACTION | 95 | 3.9265-4.4942 | 0.1903 | 145 | 0.1586 | 2900 | X-RAY DIFFRACTION | 99 | 4.4942-5.6603 | 0.1963 | 140 | 0.1474 | 2950 | X-RAY DIFFRACTION | 100 | 5.6603-44.3664 | 0.1844 | 162 | 0.1742 | 3027 | X-RAY DIFFRACTION | 97 |
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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 | 3.1062 | -0.6498 | -0.8101 | 1.5227 | 0.0713 | 0.5631 | 0.0518 | 0.281 | 0.0003 | 0.0375 | -0.0887 | -0.0449 | -0.0325 | -0.282 | 0.0339 | 0.158 | 0.034 | 0.0098 | 0.2774 | -0.0328 | 0.1165 | -11.7928 | 18.9934 | 49.2548 | 2 | 1.0435 | -0.1829 | -0.7929 | 1.5696 | 0.4482 | 6.3034 | -0.0156 | -0.1384 | 0.008 | 0.2107 | -0.0335 | -0.0955 | 0.1447 | 0.4076 | 0.04 | 0.2482 | 0.0388 | 0.0174 | 0.3848 | -0.0634 | 0.1044 | 17.994 | 6.1835 | 22.4115 | 3 | 2.0292 | -0.3605 | 0.0609 | 2.0043 | 0.364 | 3.0373 | 0.1448 | -0.265 | 0.3698 | 0.0397 | 0.1066 | 0.32 | -0.5437 | 0.1421 | -0.2226 | 0.4212 | -0.1364 | 0.1916 | 0.2568 | -0.2047 | 0.3682 | -2.8209 | -21.5283 | 29.5013 | 4 | 2.1687 | -0.5952 | 0.5174 | 1.5858 | -0.6318 | 0.8778 | 0.1206 | -0.0574 | -0.0503 | -0.2175 | -0.0773 | 0.0058 | 0.2526 | 0.2073 | -0.0394 | 0.1996 | 0.0512 | 0.0326 | 0.2774 | 0.0086 | 0.0313 | 18.6463 | -2.8023 | 58.6046 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | CHAIN A AND (RESID 58:282)2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESID 283:534)3 | X-RAY DIFFRACTION | 3 | CHAIN B AND (RESID 59:281)4 | X-RAY DIFFRACTION | 4 | CHAIN B AND (RESID 284:534) | | | |
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