ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.20.1_4487精密化 | PDB_EXTRACT | 3.27 | データ抽出 | XDS | | データ削減 | Aimless | | データスケーリング | MOLREP | | 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: 1.75→37.32 Å / SU ML: 0.21 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 20.89 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2157 | 2636 | 4.82 % |
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Rwork | 0.1817 | - | - |
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obs | 0.1833 | 54676 | 99.67 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 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: 1.75→37.32 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3974 | 0 | 61 | 272 | 4307 |
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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 | 4154 | X-RAY DIFFRACTION | f_angle_d1.207 | 5633 | X-RAY DIFFRACTION | f_dihedral_angle_d12.75 | 582 | X-RAY DIFFRACTION | f_chiral_restr0.064 | 599 | X-RAY DIFFRACTION | f_plane_restr0.007 | 721 | | | | | |
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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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1.75-1.78 | 0.4092 | 117 | 0.3301 | 2613 | X-RAY DIFFRACTION | 96 | 1.78-1.82 | 0.2473 | 157 | 0.2333 | 2681 | X-RAY DIFFRACTION | 100 | 1.82-1.85 | 0.2495 | 142 | 0.2106 | 2709 | X-RAY DIFFRACTION | 100 | 1.85-1.89 | 0.2431 | 138 | 0.2 | 2707 | X-RAY DIFFRACTION | 100 | 1.89-1.94 | 0.2568 | 139 | 0.2001 | 2732 | X-RAY DIFFRACTION | 100 | 1.94-1.99 | 0.2147 | 123 | 0.1901 | 2721 | X-RAY DIFFRACTION | 100 | 1.99-2.04 | 0.2584 | 116 | 0.184 | 2724 | X-RAY DIFFRACTION | 100 | 2.04-2.1 | 0.2321 | 166 | 0.1844 | 2697 | X-RAY DIFFRACTION | 100 | 2.1-2.17 | 0.2222 | 142 | 0.1823 | 2714 | X-RAY DIFFRACTION | 100 | 2.17-2.24 | 0.1984 | 126 | 0.1812 | 2738 | X-RAY DIFFRACTION | 100 | 2.25-2.33 | 0.2246 | 138 | 0.1803 | 2735 | X-RAY DIFFRACTION | 100 | 2.33-2.44 | 0.2455 | 147 | 0.1797 | 2729 | X-RAY DIFFRACTION | 100 | 2.44-2.57 | 0.1959 | 146 | 0.1832 | 2732 | X-RAY DIFFRACTION | 100 | 2.57-2.73 | 0.2335 | 125 | 0.1915 | 2750 | X-RAY DIFFRACTION | 100 | 2.73-2.94 | 0.2472 | 142 | 0.2054 | 2765 | X-RAY DIFFRACTION | 100 | 2.94-3.24 | 0.255 | 130 | 0.2047 | 2768 | X-RAY DIFFRACTION | 100 | 3.24-3.71 | 0.1833 | 135 | 0.1696 | 2797 | X-RAY DIFFRACTION | 100 | 3.71-4.67 | 0.1755 | 167 | 0.141 | 2781 | X-RAY DIFFRACTION | 100 | 4.67-37.32 | 0.1943 | 140 | 0.1707 | 2947 | 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 | 0.2849 | -0.2131 | -0.0584 | 0.2148 | -0.0843 | 0.3034 | 0.149 | -0.0363 | -0.2174 | -0.0801 | -0.1378 | -0.0664 | 0.3481 | -0.1938 | 0.0017 | 0.2724 | -0.0302 | -0.0185 | 0.2685 | 0.054 | 0.3157 | 11.8338 | -39.8746 | -1.0336 | 2 | 1.0839 | 0.0547 | -0.2277 | 1.5944 | -0.1751 | 0.0657 | -0.0499 | -0.0355 | -0.312 | -0.039 | -0.0788 | -0.0902 | 0.1909 | 0.1218 | -0.0363 | 0.1977 | 0.0086 | 0.0026 | 0.1509 | 0.0151 | 0.2015 | 8.9753 | -37.2217 | -6.5643 | 3 | 1.0305 | 0.0355 | -0.451 | 0.3337 | 0.2381 | 0.5765 | -0.0191 | -0.0258 | -0.1408 | 0.0151 | 0.0047 | -0.0114 | 0.0664 | -0.1518 | -0 | 0.1574 | -0.0177 | -0.0022 | 0.1569 | -0.002 | 0.1703 | -3.3394 | -24.7738 | -5.3859 | 4 | 0.6486 | 0.2165 | 0.1067 | 0.6029 | -0.0849 | 0.0541 | 0.0952 | -0.1545 | 0.2924 | 0.0623 | 0.0629 | -0.117 | -0.4057 | -0.0296 | 0.0002 | 0.3013 | -0.0035 | 0.0168 | 0.2494 | -0.0612 | 0.2696 | -1.5565 | -4.3708 | -5.1285 | 5 | 0.2295 | -0.014 | -0.0763 | 0.1411 | -0.2059 | 0.3596 | 0.0296 | -0.0899 | -0.0063 | 0.1308 | -0.0523 | -0.1888 | -0.3669 | 0.2488 | -0.0002 | 0.2423 | -0.0373 | 0.0093 | 0.1698 | -0.0117 | 0.1866 | 3.713 | -7.4606 | -5.73 | 6 | 0.4599 | -0.2612 | -0.1113 | 0.3323 | -0.0295 | 0.2928 | 0.0715 | -0.0962 | -0.0451 | -0.0997 | -0.0069 | -0.1105 | -0.0803 | -0.2053 | 0 | 0.1782 | 0.0072 | 0.0069 | 0.2015 | 0.0006 | 0.1807 | -11.8009 | -15.8013 | -7.8417 | 7 | 1.2129 | -0.2362 | -0.2282 | 1.1743 | -0.4091 | 0.5271 | -0.0067 | 0.0866 | -0.1521 | -0.0452 | -0.0289 | 0.0662 | 0.0992 | -0.1155 | -0 | 0.1516 | -0.0074 | -0.0107 | 0.1545 | -0.0193 | 0.1534 | -4.7704 | -24.141 | -10.5678 | 8 | 0.3252 | 0.1468 | 0.3168 | 1.1321 | -0.3644 | 0.5646 | -0.0893 | -0.1866 | -0.0216 | 0.092 | -0.0124 | -0.0715 | -0.0021 | 0.1332 | 0 | 0.162 | 0.0061 | -0.0214 | 0.179 | 0.0154 | 0.1443 | 7.7633 | -21.4114 | -3.8849 | 9 | 1.2734 | 0.1406 | 0.5021 | 1.5987 | -0.17 | 0.2848 | 0.0779 | -0.1133 | -0.0499 | -0.0096 | -0.0224 | -0.1374 | 0.0587 | 0.0602 | 0.0001 | 0.1355 | -0.0055 | -0.0168 | 0.1437 | 0.0093 | 0.1636 | 9.0127 | -28.0533 | -6.0859 | 10 | 0.7421 | 0.2822 | 0.2212 | 0.7851 | -0.5265 | 0.6201 | 0.0124 | 0.0181 | 0.0261 | 0.0765 | -0.0396 | -0.2237 | 0.0514 | 0.1282 | 0.0002 | 0.1752 | -0.019 | -0.0218 | 0.2108 | 0.0305 | 0.1914 | 16.4423 | -28.5411 | -1.7334 | 11 | 1.228 | -0.1036 | -0.6108 | 1.3764 | -0.1463 | 1.5829 | 0.0826 | -0.052 | 0.4495 | 0.0707 | -0.0617 | -0.0235 | -0.2833 | 0.2366 | 0.0002 | 0.2202 | -0.0248 | 0.0186 | 0.1743 | 0.0268 | 0.2789 | 24.1311 | 0.5474 | -26.208 | 12 | 0.2771 | -0.2441 | 0.2569 | 0.3172 | -0.06 | 0.456 | -0.0807 | 0.1228 | -0.3316 | -0.1402 | 0.0559 | -0.035 | 0.1572 | -0.0488 | -0.0001 | 0.2506 | 0.0214 | 0.0303 | 0.2151 | -0.035 | 0.3384 | 18.6467 | -26.9926 | -34.7411 | 13 | 0.251 | 0.1653 | -0.1067 | 0.1125 | -0.0374 | 0.206 | -0.0214 | -0.1071 | -0.2432 | 0.0826 | 0.0517 | -0.0159 | 0.0213 | 0.0364 | -0.0002 | 0.2472 | 0.0246 | 0.0261 | 0.1736 | 0.0065 | 0.267 | 19.9249 | -24.5372 | -29.1243 | 14 | 0.3827 | 0.2662 | 0.055 | 0.2321 | -0.0687 | 0.2318 | -0.1074 | 0.5521 | 0.0384 | -0.3068 | 0.0548 | 0.0693 | 0.0753 | -0.0514 | -0.0013 | 0.2728 | -0.0087 | -0.0169 | 0.3836 | 0.0311 | 0.1757 | 14.2208 | -14.1451 | -42.4444 | 15 | 1.735 | 0.4739 | -0.0068 | 0.6412 | -0.1414 | 1.8117 | 0.0144 | 0.1517 | 0.1971 | -0.0383 | -0.0277 | -0.0106 | -0.1253 | 0.0232 | 0 | 0.1777 | 0.0173 | 0.0058 | 0.1485 | 0.0394 | 0.1845 | 17.7563 | -7.6554 | -29.7455 | 16 | 0.8169 | 0.4734 | 0.4825 | 0.9502 | -0.3202 | 0.8463 | 0.1063 | -0.2187 | 0.1547 | 0.1518 | -0.079 | -0.1786 | -0.0251 | 0.3382 | 0.0005 | 0.2177 | -0.029 | -0.0168 | 0.2598 | 0.0156 | 0.2493 | 28.4711 | -4.539 | -19.6447 |
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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 22 through 38 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 39 through 58 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 59 through 83 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 84 through 105 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 106 through 119 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 120 through 141 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 142 through 194 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 195 through 218 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 219 through 243 )10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 244 through 265 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 24 through 83 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 84 through 105 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 106 through 119 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 120 through 142 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 143 through 231 )16 | X-RAY DIFFRACTION | 16 | chain 'B' | | | | | | | | | | | | | | | |
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