ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.20.1精密化 | XSCALE | | データスケーリング | XDS | | データ削減 | PHENIX | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.6→37.86 Å / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 17.14 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1783 | 3341 | 5.04 % |
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Rwork | 0.1596 | - | - |
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obs | 0.1605 | 66287 | 99.66 % |
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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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精密化ステップ | サイクル: LAST / 解像度: 1.6→37.86 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1352 | 0 | 79 | 259 | 1690 |
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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_d0.009 | 1489 | X-RAY DIFFRACTION | f_angle_d0.862 | 2026 | X-RAY DIFFRACTION | f_dihedral_angle_d17.29 | 193 | X-RAY DIFFRACTION | f_chiral_restr0.054 | 216 | X-RAY DIFFRACTION | f_plane_restr0.006 | 249 | | | | | |
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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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1.6-1.62 | 0.2567 | 139 | 0.2481 | 2586 | X-RAY DIFFRACTION | 99 | 1.62-1.65 | 0.2359 | 138 | 0.2331 | 2675 | X-RAY DIFFRACTION | 99 | 1.65-1.67 | 0.2627 | 134 | 0.228 | 2572 | X-RAY DIFFRACTION | 99 | 1.67-1.7 | 0.307 | 137 | 0.2443 | 2579 | X-RAY DIFFRACTION | 99 | 1.7-1.73 | 0.2753 | 141 | 0.2338 | 2654 | X-RAY DIFFRACTION | 99 | 1.73-1.76 | 0.2125 | 138 | 0.231 | 2640 | X-RAY DIFFRACTION | 99 | 1.76-1.79 | 0.2372 | 136 | 0.204 | 2581 | X-RAY DIFFRACTION | 99 | 1.79-1.83 | 0.1884 | 135 | 0.185 | 2588 | X-RAY DIFFRACTION | 99 | 1.83-1.87 | 0.2218 | 142 | 0.1713 | 2673 | X-RAY DIFFRACTION | 100 | 1.87-1.91 | 0.1558 | 138 | 0.1651 | 2623 | X-RAY DIFFRACTION | 99 | 1.91-1.96 | 0.1858 | 139 | 0.1627 | 2612 | X-RAY DIFFRACTION | 100 | 1.96-2.02 | 0.1691 | 137 | 0.1613 | 2608 | X-RAY DIFFRACTION | 100 | 2.02-2.08 | 0.1948 | 140 | 0.1735 | 2644 | X-RAY DIFFRACTION | 100 | 2.08-2.14 | 0.1874 | 137 | 0.1588 | 2609 | X-RAY DIFFRACTION | 100 | 2.14-2.22 | 0.1533 | 144 | 0.1436 | 2628 | X-RAY DIFFRACTION | 100 | 2.22-2.31 | 0.1482 | 142 | 0.1348 | 2648 | X-RAY DIFFRACTION | 100 | 2.31-2.41 | 0.1685 | 141 | 0.1472 | 2615 | X-RAY DIFFRACTION | 100 | 2.41-2.54 | 0.15 | 138 | 0.1475 | 2626 | X-RAY DIFFRACTION | 100 | 2.54-2.7 | 0.18 | 144 | 0.1482 | 2659 | X-RAY DIFFRACTION | 100 | 2.7-2.91 | 0.1974 | 135 | 0.1527 | 2600 | X-RAY DIFFRACTION | 100 | 2.91-3.2 | 0.1866 | 141 | 0.1551 | 2643 | X-RAY DIFFRACTION | 100 | 3.2-3.66 | 0.1707 | 139 | 0.1462 | 2612 | X-RAY DIFFRACTION | 100 | 3.66-4.61 | 0.1392 | 144 | 0.1299 | 2639 | X-RAY DIFFRACTION | 100 | 4.61-37.86 | 0.1882 | 142 | 0.181 | 2632 | X-RAY DIFFRACTION | 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 | 0.6177 | -0.5197 | -0.528 | 1.542 | 0.4037 | 0.4012 | -0.1309 | -0.1781 | 0.2412 | -0.0377 | -0.0017 | -0.0247 | -0.0982 | 0.0049 | -0.0008 | 0.2295 | 0.0331 | -0.0232 | 0.2138 | 0.0104 | 0.252 | 14.0067 | 49.1827 | 31.5862 | 2 | 0.3048 | 0.3177 | -0.141 | 0.5576 | -0.4356 | 0.3594 | 0.0763 | -0.3377 | 0.5368 | 0.0759 | -0.1709 | 0.3313 | -0.1923 | -0.203 | 0.0069 | 0.2428 | 0.0146 | 0.02 | 0.2393 | -0.0889 | 0.2667 | 8.587 | 49.5625 | 38.1075 | 3 | 0.3133 | 0.1563 | -0.2193 | 1.4254 | 0.186 | 0.1989 | -0.0568 | 0.0174 | 0.1407 | -0.1283 | -0.0408 | -0.3596 | -0.1474 | 0.0667 | 0.0003 | 0.2892 | 0.0216 | -0.0145 | 0.2016 | 0.0054 | 0.2525 | 17.5413 | 53.9199 | 30.5855 | 4 | 0.5238 | -0.3657 | -0.4539 | 1.3038 | -0.4952 | 0.7929 | -0.0984 | 0.0698 | -0.1735 | -0.2043 | 0.0231 | -0.4886 | -0.0473 | 0.0529 | -0.0047 | 0.2382 | 0.0154 | 0.025 | 0.1923 | -0.0076 | 0.2782 | 21.106 | 48.081 | 30.4484 | 5 | 0.2857 | 0.1033 | -0.1715 | 0.141 | -0.3207 | 0.5889 | -0.0644 | 0.3654 | -0.2125 | -0.3636 | -0.0424 | 0.0151 | 0.0286 | -0.0982 | 0 | 0.2808 | 0.0319 | 0.0196 | 0.2338 | -0.0303 | 0.1907 | 12.8755 | 39.5667 | 22.5385 | 6 | 0.646 | -0.3939 | 0.7692 | 1.7144 | 0.1292 | 1.0677 | 0.1107 | 0.0227 | -0.04 | -0.0334 | -0.1077 | -0.0608 | 0.1129 | -0.0389 | 0.0004 | 0.2097 | 0.0304 | -0.0072 | 0.1626 | -0.0076 | 0.1718 | 14.0324 | 37.9126 | 33.149 | 7 | 0.7117 | -0.087 | 0.6652 | 0.0814 | -0.1736 | 0.6188 | 0.0023 | 0.0225 | -0.5505 | -0.2882 | -0.0822 | -0.129 | 0.2919 | 0.0466 | 0.001 | 0.2845 | 0.0297 | 0.0319 | 0.1999 | -0.0298 | 0.303 | 14.4945 | 30.9414 | 29.7206 | 8 | 0.4513 | 0.4879 | 0.4003 | 1.0016 | 0.3268 | 0.3685 | 0.1948 | -0.03 | 0.0371 | -0.0597 | -0.1714 | -0.0896 | 0.1585 | 0.0156 | 0.0416 | 0.2189 | 0.0354 | 0.0093 | 0.2102 | 0.0201 | 0.2015 | 15.4462 | 37.0914 | 35.353 | 9 | 0.4601 | 0.0652 | -0.3324 | 0.0323 | 0.063 | 0.3659 | -0.2205 | 0.0542 | 0.1861 | -0.2372 | 0.0126 | 0.1175 | -0.4589 | -0.4657 | -0.0003 | 0.3181 | 0.0488 | -0.078 | 0.3075 | -0.0501 | 0.2981 | -7.2555 | 39.9451 | 24.6666 | 10 | 0.1744 | 0.0217 | -0.1576 | 0.1966 | -0.1577 | 0.2353 | 0.1294 | -0.0204 | 0.1105 | -0.2849 | -0.2635 | 0.2558 | 0.0416 | -0.5742 | -0.0143 | 0.304 | -0.0262 | -0.04 | 0.3686 | -0.0399 | 0.2649 | -8.0481 | 30.9558 | 17.047 | 11 | 1.1241 | 0.7094 | -0.6712 | 0.8801 | -0.7827 | 0.7037 | -0.1557 | 0.0394 | 0.0431 | -0.004 | 0.1139 | 0.3105 | 0.1931 | -0.2371 | 0.0022 | 0.2257 | -0.0361 | -0.0083 | 0.2885 | -0.0323 | 0.2822 | -6.4937 | 32.8645 | 32.3018 | 12 | 0.4781 | -0.0715 | -0.2039 | 0.2902 | -0.0921 | 1.0283 | 0.1506 | -0.6672 | 0.0243 | 0.1977 | -0.1282 | -0.0641 | 0.1511 | 0.0445 | -0.0004 | 0.2469 | -0.0092 | -0.0065 | 0.3155 | -0.0624 | 0.206 | 12.3291 | 42.882 | 45.0315 |
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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 12 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 13 through 24 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 25 through 39 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 40 through 53 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 54 through 69 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 70 through 87 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 88 through 104 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 105 through 114 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 115 through 126 )10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 127 through 133 )11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 134 through 152 )12 | X-RAY DIFFRACTION | 12 | chain 'A' and (resid 153 through 169 ) | | | | | | | | | | | |
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