ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.17.1_3678精密化 | XDS | | データ削減 | Aimless | 0.7.4データスケーリング | PHASER | 2.5.6位相決定 | PDB_EXTRACT | 3.25 | データ抽出 | | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.65→34.72 Å / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 1.01 / 位相誤差: 19.71 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2039 | 2426 | 4.83 % |
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Rwork | 0.1713 | 47832 | - |
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obs | 0.1729 | 50258 | 96.66 % |
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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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原子変位パラメータ | Biso max: 124.49 Å2 / Biso mean: 37.3254 Å2 / Biso min: 19.25 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.65→34.72 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2596 | 0 | 2 | 265 | 2863 |
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Biso mean | - | - | 25.99 | 42.85 | - |
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残基数 | - | - | - | - | 335 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.65-1.68 | 0.2818 | 176 | 0.2693 | 2822 | 2998 | 99 | 1.68-1.72 | 0.2792 | 137 | 0.2386 | 2822 | 2959 | 98 | 1.72-1.76 | 0.2363 | 137 | 0.2199 | 2830 | 2967 | 98 | 1.76-1.8 | 0.2342 | 152 | 0.2118 | 2799 | 2951 | 98 | 1.8-1.85 | 0.2553 | 136 | 0.2028 | 2810 | 2946 | 97 | 1.85-1.91 | 0.2463 | 161 | 0.19 | 2773 | 2934 | 97 | 1.91-1.97 | 0.2047 | 112 | 0.1733 | 2821 | 2933 | 97 | 1.97-2.04 | 0.199 | 146 | 0.1652 | 2888 | 3034 | 100 | 2.04-2.12 | 0.1916 | 155 | 0.1583 | 2888 | 3043 | 100 | 2.12-2.22 | 0.1978 | 127 | 0.1514 | 2896 | 3023 | 100 | 2.22-2.33 | 0.1858 | 125 | 0.1605 | 2752 | 2877 | 94 | 2.33-2.48 | 0.2158 | 131 | 0.1674 | 2612 | 2743 | 90 | 2.48-2.67 | 0.2065 | 145 | 0.1764 | 2748 | 2893 | 94 | 2.67-2.94 | 0.2151 | 160 | 0.1822 | 2910 | 3070 | 100 | 2.94-3.37 | 0.2245 | 132 | 0.1824 | 2716 | 2848 | 92 | 3.37-4.24 | 0.176 | 138 | 0.1478 | 2920 | 3058 | 98 | 4.24-34.72 | 0.1927 | 156 | 0.1708 | 2825 | 2981 | 91 |
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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 | 1.1999 | -0.3568 | -0.1657 | 0.5856 | 1.0694 | 2.1638 | 0.1054 | 0.0897 | 0.1392 | -0.2045 | -0.0096 | -0.1653 | -0.3828 | 0.1865 | -0.0483 | 0.3172 | -0.0201 | -0.0009 | 0.2351 | 0.0258 | 0.2764 | -12.7347 | 23.5033 | -8.3852 | 2 | 1.9899 | 1.0721 | -1.5265 | 2.9456 | -1.8502 | 4.1864 | -0.1818 | 0.0888 | -0.2519 | -0.3508 | 0.1098 | -0.2119 | 0.5956 | -0.1728 | 0.0768 | 0.3019 | -0.0173 | 0.0189 | 0.2115 | -0.0154 | 0.2836 | -16.3599 | 13.7332 | -8.0099 | 3 | 2.2949 | 0.8066 | -0.0758 | 1.3399 | 0.3403 | 0.6997 | 0.1466 | -0.2635 | 0.1974 | 0.1665 | -0.1253 | 0.0624 | -0.008 | 0.0363 | -0.0269 | 0.3079 | -0.0414 | -0.009 | 0.2761 | 0.0032 | 0.278 | -18.2006 | 25.0026 | 6.2345 | 4 | 1.1361 | -0.0365 | -0.1863 | 1.1406 | -0.1787 | 3.2431 | 0.1014 | -0.0507 | -0.0305 | -0.141 | -0.0756 | -0.3327 | -0.052 | 0.567 | -0.0152 | 0.2688 | -0.0012 | 0.0283 | 0.2715 | 0.0282 | 0.3523 | -4.2912 | 21.0796 | -5.7169 | 5 | 3.9077 | 3.029 | 0.2427 | 9.2159 | -0.6851 | 5.4709 | 0.0235 | -1.0547 | -0.0824 | 0.3629 | -0.0571 | -0.07 | 0.3734 | 0.4742 | 0.1132 | 0.3991 | -0.054 | -0.0298 | 0.4538 | 0.0815 | 0.2866 | -17.7035 | 17.4973 | 14.8398 | 6 | 1.1756 | 0.3896 | -0.6885 | 1.308 | -1.4275 | 4.1808 | -0.1222 | 0.0276 | -0.2282 | -0.3805 | 0.0188 | -0.3196 | 0.5964 | 0.1407 | 0.092 | 0.3791 | -0.0225 | 0.0838 | 0.2247 | -0.024 | 0.362 | -5.7461 | 17.2014 | -16.4703 | 7 | 2.4357 | 0.6672 | -1.8851 | 3.0449 | -2.5303 | 6.2791 | -0.1211 | -0.1265 | -0.2871 | -0.13 | -0.0709 | -0.4447 | 0.4154 | 0.2923 | 0.1716 | 0.3295 | 0.0642 | 0.0062 | 0.2152 | 0.0053 | 0.4078 | -6.9037 | 11.4326 | -6.7396 | 8 | 6.0048 | -0.194 | 2.3888 | 2.3109 | -0.8387 | 3.1797 | 0.0703 | 0.0125 | -0.1052 | 0.1695 | 0.0689 | -0.126 | -0.2133 | 0.8308 | -0.2437 | 0.2562 | -0.0459 | 0.02 | 0.3627 | -0.0248 | 0.186 | -4.2435 | 46.4352 | 10.4594 | 9 | 5.794 | -1.5905 | 4.8777 | 5.6308 | -1.055 | 4.1252 | 0.0296 | -1.2493 | 0.2396 | 0.9637 | -0.3825 | -0.7397 | -0.2928 | 0.3848 | 0.3841 | 0.3967 | -0.0766 | -0.0421 | 0.4756 | 0.0012 | 0.3831 | 11.4766 | 54.5112 | 14.0507 | 10 | 2.5138 | -0.4599 | 1.0374 | 1.5262 | -0.1704 | 0.8595 | -0.0661 | -0.2065 | 0.0613 | 0.0538 | 0.045 | 0.1122 | -0.0492 | -0.0079 | 0.0375 | 0.2536 | -0.0194 | 0.0018 | 0.2458 | 0.0078 | 0.2149 | -7.8611 | 47.9204 | 7.8103 | 11 | 4.8029 | 0.3392 | -2.5619 | 4.6709 | -2.8093 | 8.7694 | -0.0329 | -0.5221 | -0.0287 | 0.5433 | 0.4418 | 0.4235 | 0.0602 | -0.6183 | -0.4612 | 0.287 | 0.0168 | 0.0186 | 0.3578 | 0.0527 | 0.3147 | -20.7378 | 45.5346 | 10.1016 | 12 | 5.517 | 0.7866 | 0.8551 | 1.6702 | -0.6191 | 1.4084 | 0.0659 | -0.4159 | 0.0861 | -0.0225 | -0.2017 | -0.2839 | 0.0919 | 0.1874 | 0.0792 | 0.2374 | -0.0151 | 0.0081 | 0.3139 | 0.0443 | 0.2215 | 1.3918 | 42.2232 | 10.6829 | 13 | 4.8757 | -4.1667 | -4.0885 | 5.9813 | 4.2591 | 3.7338 | -0.1092 | -0.325 | -0.2176 | 0.2159 | 0.534 | 0.2939 | 1.0215 | 0.1466 | -0.3344 | 0.5665 | 0.1438 | 0.0358 | 0.7394 | 0.1535 | 0.7535 | 23.4452 | 36.8909 | 7.942 | 14 | 1.4883 | -0.4428 | -0.5476 | 0.9951 | -0.1131 | 1.5163 | 0.0546 | -0.6955 | -0.3435 | 0.0672 | -0.0169 | 0.1471 | 0.1026 | -0.1381 | -0.0204 | 0.261 | -0.0474 | -0.0033 | 0.2614 | 0.047 | 0.2642 | -7.4211 | 38.7379 | 7.9999 | 15 | 2.6904 | 0.9523 | 0.9136 | 1.6544 | 0.0719 | 0.7177 | -0.168 | 0.317 | 0.1153 | -0.2408 | 0.0651 | -0.1185 | -0.0522 | 0.1639 | 0.0833 | 0.2698 | -0.0301 | 0.0048 | 0.3252 | 0.0622 | 0.2959 | 9.9683 | 47.4037 | 4.6221 | 16 | 7.1233 | 2.2183 | 2.0928 | 2.6141 | 0.6214 | 2.4981 | -0.1428 | 0.2387 | -0.0637 | -0.2399 | 0.0894 | -0.0798 | 0.0495 | 0.2583 | 0.1095 | 0.2286 | -0.007 | 0.0155 | 0.213 | 0.0155 | 0.1646 | 1.2802 | 42.187 | -0.402 |
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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 43 through 65 )A43 - 65 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 66 through 86 )A66 - 86 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 87 through 118 )A87 - 118 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 119 through 149 )A119 - 149 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 150 through 155 )A150 - 155 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 156 through 189 )A156 - 189 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 190 through 213 )A190 - 213 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 42 through 58 )B42 - 58 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 59 through 65 )B59 - 65 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 66 through 107 )B66 - 107 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 108 through 118 )B108 - 118 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 119 through 130 )B119 - 130 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 131 through 137 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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