ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.10_2155: ???)精密化 | HKL-3000 | | データ削減 | HKL-3000 | | 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: 4JON 解像度: 1.08→20.487 Å / SU ML: 0.09 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 17.21
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1786 | 2000 | 3.72 % |
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Rwork | 0.1639 | - | - |
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obs | 0.1644 | 53761 | 99.6 % |
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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 |
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精密化ステップ | サイクル: LAST / 解像度: 1.08→20.487 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1090 | 0 | 0 | 235 | 1325 |
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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_d0.007 | 1114 | X-RAY DIFFRACTION | f_angle_d0.935 | 1505 | X-RAY DIFFRACTION | f_dihedral_angle_d14.104 | 418 | X-RAY DIFFRACTION | f_chiral_restr0.091 | 166 | X-RAY DIFFRACTION | f_plane_restr0.008 | 197 | | | | | |
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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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1.0803-1.1073 | 0.2771 | 139 | 0.2658 | 3571 | X-RAY DIFFRACTION | 97 | 1.1073-1.1372 | 0.1957 | 140 | 0.2016 | 3648 | X-RAY DIFFRACTION | 100 | 1.1372-1.1707 | 0.1925 | 141 | 0.1801 | 3663 | X-RAY DIFFRACTION | 100 | 1.1707-1.2084 | 0.2119 | 142 | 0.1823 | 3661 | X-RAY DIFFRACTION | 100 | 1.2084-1.2516 | 0.1856 | 142 | 0.1786 | 3672 | X-RAY DIFFRACTION | 100 | 1.2516-1.3017 | 0.1779 | 142 | 0.1675 | 3677 | X-RAY DIFFRACTION | 100 | 1.3017-1.361 | 0.1607 | 142 | 0.1653 | 3676 | X-RAY DIFFRACTION | 100 | 1.361-1.4327 | 0.1579 | 143 | 0.1595 | 3699 | X-RAY DIFFRACTION | 100 | 1.4327-1.5224 | 0.1732 | 142 | 0.1542 | 3695 | X-RAY DIFFRACTION | 100 | 1.5224-1.6399 | 0.1875 | 143 | 0.1499 | 3704 | X-RAY DIFFRACTION | 100 | 1.6399-1.8049 | 0.1663 | 144 | 0.1496 | 3724 | X-RAY DIFFRACTION | 100 | 1.8049-2.0659 | 0.1876 | 145 | 0.1458 | 3740 | X-RAY DIFFRACTION | 100 | 2.0659-2.6019 | 0.1497 | 146 | 0.1545 | 3783 | X-RAY DIFFRACTION | 100 | 2.6019-20.491 | 0.1879 | 149 | 0.1711 | 3848 | X-RAY DIFFRACTION | 98 |
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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 | 6.9917 | 2.0832 | 3.7273 | 3.0919 | 1.8976 | 6.0295 | -0.1264 | 0.1005 | 0.1853 | -0.1142 | 0.0636 | 0.212 | -0.1116 | -0.0892 | 0.0723 | 0.0874 | 0.0087 | 0.003 | 0.0762 | 0.0032 | 0.0841 | -19.0975 | 4.2469 | 10.9192 | 2 | 4.0807 | 0.1552 | 0.3622 | 0.0267 | -0.1239 | 2.6082 | -0.0159 | -0.3943 | 0.2819 | 0.0125 | -0.0167 | -0.0207 | 0.0771 | -0.0632 | 0.038 | 0.1065 | -0.0049 | -0.0002 | 0.1255 | -0.0381 | 0.0787 | -7.9101 | 8.1183 | 18.6404 | 3 | 2.7601 | 0.004 | 0.1303 | 1.7188 | 0.6376 | 1.231 | 0.0452 | 0.1407 | 0.0809 | -0.1924 | -0.0547 | 0.0427 | -0.152 | -0.0279 | 0.0192 | 0.1091 | 0.0001 | -0.0043 | 0.0651 | 0.0135 | 0.0631 | -14.4205 | 5.5052 | 4.1525 | 4 | 2.3809 | 0.8333 | -0.5461 | 1.9196 | -0.2656 | 2.3633 | 0.0865 | 0.5066 | 0.384 | -0.3651 | 0.1903 | 0.2687 | -0.2432 | -0.2474 | -0.2687 | 0.1675 | -0.0078 | 0.0129 | 0.1434 | 0.0547 | 0.1751 | -8.9484 | 13.7924 | 3.1813 | 5 | 2.472 | 0.2132 | 0.1445 | 1.7599 | 0.3966 | 1.0131 | -0.0247 | 0.0303 | 0.0642 | -0.1756 | 0.0694 | -0.1891 | -0.0647 | 0.101 | -0.0489 | 0.0974 | -0.0043 | 0.0133 | 0.0691 | 0.0045 | 0.0549 | -6.7793 | 3.4063 | 4.9844 | 6 | 2.2026 | -0.0833 | 0.0242 | 1.8408 | -0.036 | 1.8073 | -0.0164 | 0.0406 | -0.1215 | -0.1391 | 0.0544 | -0.0803 | 0.1016 | 0.0694 | -0.0374 | 0.0846 | 0.0087 | 0.0098 | 0.051 | -0.0099 | 0.0668 | -7.9048 | -6.2857 | 7.678 | 7 | 3.3174 | 1.7865 | 0.1761 | 1.1178 | 0.1048 | -0.0025 | 0.0976 | -0.1033 | -0.1524 | 0.0259 | -0.0564 | 0.0181 | -0.0076 | -0.0207 | -0.0379 | 0.1117 | 0.0005 | 0.0072 | 0.121 | -0.0236 | 0.1727 | 9.1374 | 6.9733 | 16.5022 | 8 | 6.1779 | 1.7291 | 2.2734 | 0.6333 | 0.7844 | 0.9713 | 0.0426 | -0.1685 | -0.0825 | 0.0358 | 0.001 | 0.0284 | -0.0026 | -0.0157 | -0.056 | 0.08 | 0.0121 | -0.0018 | 0.0882 | -0.0052 | 0.0921 | -14.9445 | 0.995 | 14.8649 | 9 | 4.0262 | -1.6192 | 1.7082 | 3.2224 | -1.1911 | 3.6064 | 0.0199 | -0.3921 | -0.5037 | 0.1115 | 0.1193 | 0.567 | 0.2482 | -0.3724 | -0.1042 | 0.121 | -0.0127 | 0.0227 | 0.1446 | 0.0127 | 0.214 | -24.6069 | -5.5884 | 13.4013 |
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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 2 through 10 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 11 through 19 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 20 through 32 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 33 through 43 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 44 through 61 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 62 through 105 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 106 through 120 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 121 through 128 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 129 through 139 ) | | | | | | | | |
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