ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | PHENIX | 1.8.3_1479精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | HKL-2000 | | データ削減 | | HKL-2000 | | データスケーリング | | PHENIX | | 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: PDB ENTRY 3QLK 解像度: 2.4→39.7 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0 / 位相誤差: 18.16 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.192 | 1986 | 5.47 % |
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Rwork | 0.151 | - | - |
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obs | 0.154 | 36306 | 98.7 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso mean: 36.61 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.4→39.7 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6796 | 0 | 0 | 320 | 7116 |
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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_d0.004 | 6926 | X-RAY DIFFRACTION | f_angle_d0.901 | 9398 | X-RAY DIFFRACTION | f_dihedral_angle_d13.066 | 2576 | X-RAY DIFFRACTION | f_chiral_restr0.035 | 1076 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1234 | | | | | |
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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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2.3984-2.4584 | 0.231 | 135 | 0.1631 | 2330 | X-RAY DIFFRACTION | 95 | 2.4584-2.5248 | 0.233 | 140 | 0.1645 | 2435 | X-RAY DIFFRACTION | 97 | 2.5248-2.5991 | 0.2089 | 142 | 0.166 | 2414 | X-RAY DIFFRACTION | 98 | 2.5991-2.683 | 0.2166 | 138 | 0.1695 | 2404 | X-RAY DIFFRACTION | 98 | 2.683-2.7789 | 0.2344 | 142 | 0.17 | 2441 | X-RAY DIFFRACTION | 98 | 2.7789-2.8901 | 0.1976 | 142 | 0.1738 | 2455 | X-RAY DIFFRACTION | 99 | 2.8901-3.0216 | 0.219 | 141 | 0.172 | 2461 | X-RAY DIFFRACTION | 99 | 3.0216-3.1808 | 0.1998 | 143 | 0.1689 | 2453 | X-RAY DIFFRACTION | 99 | 3.1808-3.38 | 0.2273 | 144 | 0.1695 | 2471 | X-RAY DIFFRACTION | 100 | 3.38-3.6408 | 0.1994 | 142 | 0.157 | 2469 | X-RAY DIFFRACTION | 100 | 3.6408-4.0069 | 0.1847 | 144 | 0.1462 | 2480 | X-RAY DIFFRACTION | 100 | 4.0069-4.586 | 0.1564 | 144 | 0.1188 | 2489 | X-RAY DIFFRACTION | 99 | 4.586-5.775 | 0.1716 | 143 | 0.1298 | 2499 | X-RAY DIFFRACTION | 100 | 5.775-39.7076 | 0.1497 | 146 | 0.1397 | 2519 | X-RAY DIFFRACTION | 99 |
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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 | 1.5428 | 0.5375 | 0.0846 | 1.1008 | 0.1217 | 0.7247 | -0.0965 | 0.0806 | -0.0477 | -0.0745 | 0.0891 | -0.1605 | -0.0269 | 0.0848 | 0.0089 | 0.1694 | -0.0258 | 0.0144 | 0.1736 | -0.0065 | 0.1841 | -29.8573 | 29.7218 | -12.9533 | 2 | 0.0396 | -0.2167 | 0.1045 | 1.0058 | -0.6613 | 1.2083 | -0.0085 | 0.0363 | -0.1072 | -0.0944 | -0.0267 | -0.1183 | 0.135 | 0.0879 | 0.0269 | 0.1713 | -0.0084 | 0.0211 | 0.1775 | -0.0296 | 0.2297 | -35.4085 | 6.0555 | -8.0795 | 3 | 1.617 | -0.618 | 0.3444 | 0.9325 | -0.3995 | 0.9838 | -0.0342 | -0.0445 | 0.2142 | 0.1282 | -0.008 | -0.3034 | -0.0806 | 0.1051 | 0.069 | 0.2252 | 0.0199 | -0.021 | 0.2005 | -0.0186 | 0.2769 | -28.5269 | 1.5877 | 11.8335 | 4 | 0.9751 | -0.0487 | -0.048 | 1.1179 | -0.1494 | 0.7192 | -0.0554 | -0.2958 | -0.0911 | 0.1463 | 0.1058 | 0.0803 | 0.0006 | 0.0566 | -0.0381 | 0.1858 | 0.0436 | 0.011 | 0.241 | 0.0292 | 0.1391 | -53.3894 | 10.8893 | 29.6799 | 5 | 1.8335 | 0.5993 | -0.2791 | 0.8245 | 0.1437 | 0.5738 | 0.0389 | -0.1026 | -0.0318 | 0.0917 | 0.0687 | -0.2279 | -0.0736 | 0.2619 | -0.0684 | 0.2425 | -0.0066 | -0.018 | 0.2479 | -0.0459 | 0.2059 | -35.821 | 26.7472 | 18.088 |
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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 1 through 189 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 190 through 342 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 343 through 440 )4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 1 through 296 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 297 through 440 ) | | | | |
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