ソフトウェア | 名称 | バージョン | 分類 |
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ADSC | Quantumデータ収集 | PHASER | | 位相決定 | PHENIX | (phenix.refine: 1.8_1063)精密化 | XDS | | データ削減 | Aimless | | 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: 3HMC 解像度: 1.1→36.661 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.07 / σ(F): 1.98 / 位相誤差: 12.89 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1428 | 3950 | 5.01 % | RANDOM |
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Rwork | 0.1344 | - | - | - |
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all | 0.1348 | 78870 | - | - |
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obs | 0.1348 | 78870 | 98.17 % | - |
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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 max: 48.39 Å2 / Biso mean: 11.511 Å2 / Biso min: 3.53 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.1→36.661 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1630 | 0 | 0 | 345 | 1975 |
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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 | 1713 | X-RAY DIFFRACTION | f_angle_d1.229 | 2320 | X-RAY DIFFRACTION | f_chiral_restr0.073 | 245 | X-RAY DIFFRACTION | f_plane_restr0.006 | 302 | X-RAY DIFFRACTION | f_dihedral_angle_d12.187 | 638 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.1-1.1134 | 0.2426 | 102 | 0.2192 | 2220 | 2322 | 78 | 1.1134-1.1275 | 0.2134 | 110 | 0.2008 | 2317 | 2427 | 86 | 1.1275-1.1424 | 0.1781 | 135 | 0.1859 | 2531 | 2666 | 92 | 1.1424-1.158 | 0.1781 | 125 | 0.1684 | 2555 | 2680 | 95 | 1.158-1.1745 | 0.1728 | 152 | 0.1602 | 2742 | 2894 | 99 | 1.1745-1.1921 | 0.164 | 143 | 0.1524 | 2693 | 2836 | 100 | 1.1921-1.2107 | 0.165 | 151 | 0.1468 | 2726 | 2877 | 100 | 1.2107-1.2306 | 0.1498 | 156 | 0.1448 | 2680 | 2836 | 100 | 1.2306-1.2518 | 0.1702 | 145 | 0.1408 | 2746 | 2891 | 100 | 1.2518-1.2745 | 0.1586 | 151 | 0.1347 | 2723 | 2874 | 100 | 1.2745-1.2991 | 0.1334 | 113 | 0.1324 | 2727 | 2840 | 100 | 1.2991-1.3256 | 0.1537 | 146 | 0.1336 | 2759 | 2905 | 100 | 1.3256-1.3544 | 0.1377 | 149 | 0.1282 | 2675 | 2824 | 100 | 1.3544-1.3859 | 0.1267 | 139 | 0.1269 | 2757 | 2896 | 100 | 1.3859-1.4206 | 0.1298 | 154 | 0.1263 | 2686 | 2840 | 100 | 1.4206-1.459 | 0.1609 | 160 | 0.1209 | 2761 | 2921 | 100 | 1.459-1.5019 | 0.1303 | 148 | 0.1196 | 2698 | 2846 | 100 | 1.5019-1.5504 | 0.115 | 133 | 0.1138 | 2725 | 2858 | 100 | 1.5504-1.6058 | 0.139 | 133 | 0.113 | 2707 | 2840 | 100 | 1.6058-1.6701 | 0.1328 | 142 | 0.1184 | 2739 | 2881 | 100 | 1.6701-1.7461 | 0.1168 | 139 | 0.1158 | 2721 | 2860 | 100 | 1.7461-1.8382 | 0.1308 | 166 | 0.1235 | 2741 | 2907 | 100 | 1.8382-1.9533 | 0.1248 | 127 | 0.1203 | 2714 | 2841 | 100 | 1.9533-2.1041 | 0.1215 | 157 | 0.1223 | 2725 | 2882 | 100 | 2.1041-2.3158 | 0.1244 | 143 | 0.125 | 2699 | 2842 | 100 | 2.3158-2.6509 | 0.1539 | 138 | 0.1357 | 2750 | 2888 | 100 | 2.6509-3.3395 | 0.1523 | 153 | 0.1411 | 2697 | 2850 | 100 | 3.3395-36.6809 | 0.1425 | 140 | 0.1439 | 2706 | 2846 | 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 | 2.3274 | -1.626 | 0.9175 | 1.5382 | -0.6585 | 0.3624 | -0.1148 | -0.5066 | 0.0304 | 0.0385 | 0.1544 | 0.1515 | -0.0153 | -0.2184 | 0.0074 | 0.0673 | -0.007 | -0.0031 | 0.1213 | 0.0011 | 0.0594 | -15.7838 | 6.2983 | 6.4507 | 2 | 1.6432 | -0.2151 | 1.1625 | 2.1328 | -0.1794 | 2.313 | 0.0835 | -0.0973 | -0.0516 | 0.2439 | -0.0495 | 0.0798 | 0.1042 | -0.0303 | -0.0755 | 0.0901 | -0.0192 | -0.0039 | 0.046 | -0.0009 | 0.025 | -5.8326 | -3.7915 | 9.0661 | 3 | 1.8609 | 1.0665 | -0.1827 | 1.3309 | -0.2659 | 0.5623 | 0.0439 | -0.0062 | -0.135 | 0.0564 | -0.0387 | -0.1272 | 0.0476 | 0.0543 | -0.0076 | 0.052 | -0.0052 | -0.0103 | 0.041 | -0.0078 | 0.036 | 3.7876 | -0.0691 | 1.6434 | 4 | 2.8529 | 3.1009 | 0.718 | 4.3842 | 0.8622 | 0.7145 | -0.0647 | 0.1601 | -0.2427 | -0.0777 | 0.075 | -0.2797 | 0.058 | 0.0842 | -0.0096 | 0.0502 | -0.0046 | 0.0067 | 0.0653 | -0.0188 | 0.0579 | 10.0546 | 1.7998 | -7.5106 | 5 | 1.0683 | 0.4013 | 0.0014 | 1.1287 | 0.0037 | 0.6107 | 0.0095 | -0.0065 | 0.026 | 0.0093 | -0.0002 | -0.0783 | -0.0637 | 0.0792 | -0.0149 | 0.0537 | -0.0165 | 0.0003 | 0.0556 | -0.0018 | 0.035 | 7.5919 | 11.9121 | -5.3446 | 6 | 1.4331 | 0.2641 | -0.214 | 3.0418 | 0.873 | 1.3443 | 0.0616 | -0.0404 | 0.1535 | 0.0102 | 0.0002 | 0.033 | -0.219 | 0.0409 | 0.046 | 0.0566 | -0.0188 | 0.0131 | 0.0459 | 0.001 | 0.0554 | 0.5074 | 16.7358 | 0.1749 | 7 | 0.7447 | 0.0971 | 0.1733 | 0.6802 | 0.0436 | 0.4178 | 0.0485 | 0.0244 | 0.1734 | 0.0396 | 0.041 | 0.0032 | -0.1899 | 0.042 | -0.0559 | 0.0758 | -0.0143 | 0.0145 | 0.038 | -0.0034 | 0.0621 | -1.1262 | 18.4908 | 0.8009 | 8 | 0.8468 | -0.6287 | 0.5511 | 1.705 | 0.0823 | 3.0818 | 0.0465 | -0.0338 | 0.1151 | 0.1202 | 0.076 | 0.1438 | -0.1943 | -0.1464 | -0.1066 | 0.0666 | 0.0042 | 0.0245 | 0.0495 | -0.0013 | 0.0717 | -9.0775 | 16.1847 | 8.2319 | 9 | 2.0427 | 0.8899 | 1.4692 | 4.0826 | 0.3119 | 3.5848 | 0.0521 | -0.116 | -0.0308 | 0.2986 | -0.0015 | 0.2371 | 0.2437 | -0.029 | -0.02 | 0.1051 | 0.004 | 0.0034 | 0.0811 | 0.0104 | 0.038 | -6.3636 | 0.8191 | 16.1541 | 10 | 2.96 | -0.3001 | 0.3995 | 2.8447 | 0.4508 | 2.4063 | 0.0201 | 0.1784 | 0.018 | -0.2014 | -0.0175 | 0.1624 | -0.0562 | -0.2361 | 0.0085 | 0.0367 | -0.0148 | -0.003 | 0.06 | 0.0128 | 0.0548 | -12.0184 | 8.274 | -1.6963 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND RESID -3:7 ) | A-3 - 7 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 8:24 )A8 - 24 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 25:65 )A25 - 65 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 66:86 )A66 - 86 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN A AND RESID 87:122 )A87 - 122 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN A AND RESID 123:137 )A123 - 137 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN A AND RESID 138:156 )A138 - 156 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN A AND RESID 157:174 )A157 - 174 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN A AND RESID 175:186 )A175 - 186 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN A AND RESID 187:202 )A187 - 202 | | | | | | | | | | | | | | | | | | | |
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