ソフトウェア | 名称 | バージョン | 分類 | NB |
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XSCALE | | データスケーリング | | PHENIX | (dev_2621: ???)精密化 | | PDB_EXTRACT | 3.22 | データ抽出 | | XDS | | データ削減 | | MoRDa | | 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: 3INP 解像度: 1.4→40.684 Å / SU ML: 0.13 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 15.8
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1648 | 2019 | 1.52 % |
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Rwork | 0.1484 | - | - |
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obs | 0.1487 | 132647 | 99.87 % |
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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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原子変位パラメータ | Biso max: 72.43 Å2 / Biso mean: 18.9641 Å2 / Biso min: 7.5 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.4→40.684 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5028 | 0 | 48 | 806 | 5882 |
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Biso mean | - | - | 41.58 | 31.34 | - |
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残基数 | - | - | - | - | 670 |
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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_d0.005 | 5530 | X-RAY DIFFRACTION | f_angle_d0.844 | 7582 | X-RAY DIFFRACTION | f_chiral_restr0.087 | 875 | X-RAY DIFFRACTION | f_plane_restr0.006 | 995 | X-RAY DIFFRACTION | f_dihedral_angle_d18.589 | 2111 | | | | | |
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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: 14 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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1.4-1.435 | 0.2483 | 174 | 0.2313 | 9262 | 9436 | 1.435-1.4738 | 0.2302 | 166 | 0.2062 | 9304 | 9470 | 1.4738-1.5172 | 0.2253 | 164 | 0.1889 | 9252 | 9416 | 1.5172-1.5662 | 0.1774 | 138 | 0.1686 | 9315 | 9453 | 1.5662-1.6221 | 0.1869 | 139 | 0.1566 | 9258 | 9397 | 1.6221-1.6871 | 0.162 | 134 | 0.1535 | 9379 | 9513 | 1.6871-1.7639 | 0.1953 | 133 | 0.1539 | 9270 | 9403 | 1.7639-1.8569 | 0.1727 | 133 | 0.1506 | 9359 | 9492 | 1.8569-1.9732 | 0.1673 | 138 | 0.1432 | 9328 | 9466 | 1.9732-2.1256 | 0.1698 | 133 | 0.1418 | 9294 | 9427 | 2.1256-2.3394 | 0.1703 | 144 | 0.1433 | 9331 | 9475 | 2.3394-2.6779 | 0.1638 | 126 | 0.1429 | 9382 | 9508 | 2.6779-3.3736 | 0.1504 | 142 | 0.1432 | 9409 | 9551 | 3.3736-40.7008 | 0.1342 | 155 | 0.1352 | 9485 | 9640 |
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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 | 2.4836 | -0.5606 | -1.343 | 2.2984 | 1.5118 | 3.6354 | 0.0191 | -0.1228 | -0.1561 | 0.0932 | -0.0193 | 0.0453 | 0.148 | 0.0181 | -0.0396 | 0.1441 | 0.0052 | -0.0197 | 0.104 | 0.0385 | 0.1466 | 1.2173 | -7.3637 | 16.2059 | 2 | 4.0442 | 1.2144 | -4.0406 | 0.3987 | -1.1558 | 9.2025 | -0.0427 | 0.1417 | -0.1519 | -0.0256 | -0.0114 | -0.1007 | 0.0737 | -0.0621 | 0.1103 | 0.1501 | 0.0135 | -0.0338 | 0.0683 | 0.0063 | 0.1702 | 0.8322 | -14.256 | 6.9067 | 3 | 0.5978 | 0.4121 | -0.1666 | 0.9819 | -0.2377 | 0.7608 | 0.0048 | -0.0215 | -0.1218 | -0.0315 | 0.0112 | -0.0235 | 0.1385 | -0.0041 | -0.0153 | 0.1193 | -0.0001 | -0.0046 | 0.0791 | 0.0078 | 0.1033 | -2.851 | -1.8254 | 7.6969 | 4 | 2.0868 | 0.3111 | 0.1459 | 2.7668 | 0.8155 | 1.1843 | 0.0166 | -0.0179 | -0.0198 | -0.0583 | -0.0091 | 0.1179 | -0.0111 | -0.101 | -0.0047 | 0.0836 | -0.0009 | -0.0044 | 0.092 | 0.0182 | 0.0655 | -10.1307 | 8.6972 | 11.7839 | 5 | 6.5154 | -0.5707 | -0.6014 | 1.4845 | -0.4544 | 0.9415 | 0.0462 | -0.0804 | -0.0266 | 0.025 | -0.0588 | -0.0881 | 0.0402 | 0.0047 | 0.0084 | 0.137 | -0.0088 | -0.0199 | 0.1233 | 0.0058 | 0.0605 | 0.4353 | 9.1733 | 21.0448 | 6 | 4.0508 | -0.269 | -2.5654 | 1.7655 | 0.1173 | 1.6357 | -0.063 | -0.2562 | -0.0517 | 0.3745 | -0.0084 | -0.0033 | 0.0091 | -0.2415 | 0.0777 | 0.2366 | -0.0056 | 0.0012 | 0.2652 | 0.0234 | 0.0591 | -1.2268 | 7.9694 | 31.5938 | 7 | 3.7031 | -1.2369 | -1.2876 | 2.6259 | 0.861 | 2.9169 | 0.0402 | -0.24 | -0.2131 | 0.2648 | 0.0258 | -0.1269 | 0.145 | -0.0339 | -0.0429 | 0.1656 | -0.0355 | -0.0237 | 0.1054 | 0.0472 | 0.0955 | 1.704 | -0.8812 | 26.4493 | 8 | 2.2525 | 0.2643 | -1.1646 | 2.9642 | 2.3818 | 4.9954 | 0.022 | 0.027 | -0.1559 | 0.1445 | 0.1233 | -0.3375 | 0.1281 | 0.1431 | -0.1438 | 0.1409 | 0.0024 | -0.0319 | 0.1275 | 0.0384 | 0.1604 | 5.4781 | -8.6235 | 18.6583 | 9 | 3.8079 | -1.2706 | -0.7542 | 3.2586 | -2.0682 | 4.727 | 0.0124 | -0.4684 | -0.225 | 0.4956 | 0.1362 | -0.1644 | -0.0859 | 0.0215 | -0.0917 | 0.2369 | -0.0108 | -0.0868 | 0.1694 | 0.0938 | 0.2006 | 5.456 | -13.8466 | 25.4987 | 10 | 1.5772 | 0.4797 | -1.0912 | 2.4055 | -0.9656 | 1.3849 | -0.0062 | -0.1176 | 0.0753 | 0.0657 | 0.0477 | -0.1128 | -0.0254 | 0.0733 | -0.0614 | 0.1253 | -0.0189 | -0.0239 | 0.1471 | -0.0466 | 0.1639 | 24.8196 | 37.8058 | 16.2513 | 11 | 3.4195 | -1.7026 | 4.9487 | 1.2375 | -1.6776 | 8.9857 | 0.0474 | 0.0643 | 0.1178 | -0.0408 | -0.0486 | -0.0473 | -0.1098 | 0.171 | 0.0247 | 0.1082 | -0.0393 | 0.0031 | 0.133 | -0.024 | 0.1759 | 30.9992 | 40.9046 | 6.9599 | 12 | 1.1907 | -0.041 | 0.0409 | 0.1497 | -0.0912 | 0.4893 | -0.0053 | -0.0047 | 0.0529 | 0.0104 | 0.0185 | -0.064 | -0.0603 | 0.1024 | -0.0107 | 0.0936 | -0.0173 | -0.0092 | 0.121 | -0.0105 | 0.1183 | 22.2023 | 31.4251 | 7.9547 | 13 | 8.1032 | 0.681 | -0.1963 | 3.6762 | -0.6215 | 2.5293 | -0.0709 | 0.2314 | -0.2287 | -0.1554 | 0.066 | -0.0377 | 0.1723 | 0.0081 | 0.0126 | 0.1054 | -0.0084 | -0.0036 | 0.0806 | -0.0167 | 0.0628 | 17.0259 | 20.9661 | 5.8126 | 14 | 3.0896 | 0.3113 | -0.7064 | 2.4491 | -0.1538 | 1.2849 | -0.0277 | -0.0574 | -0.1284 | 0.0332 | 0.0369 | -0.1038 | 0.0517 | 0.0965 | -0.0074 | 0.0858 | 0.0048 | -0.0209 | 0.0962 | -0.0046 | 0.064 | 16.3915 | 19.5395 | 14.4904 | 15 | 2.1496 | -1.507 | 0.6941 | 7.1675 | -1.0002 | 1.0276 | -0.0099 | -0.0729 | 0.1478 | -0.0161 | -0.0015 | -0.0497 | -0.0327 | 0.0282 | 0.0049 | 0.1007 | 0.0011 | -0.006 | 0.1408 | -0.0371 | 0.0603 | 10.8561 | 28.8967 | 21.1129 | 16 | 4.157 | -3.124 | 2.1337 | 3.5516 | -2.6717 | 3.1893 | 0.0349 | -0.4357 | -0.0404 | 0.2506 | -0.0491 | 0.0333 | 0.2345 | -0.0433 | 0.0604 | 0.2189 | -0.0259 | -0.0263 | 0.2735 | -0.0129 | 0.0901 | 12.7306 | 27.7856 | 31.841 | 17 | 1.8967 | 0.5582 | -0.5745 | 1.5262 | -0.2164 | 1.4561 | 0.1092 | -0.2518 | 0.2343 | 0.1429 | -0.0354 | 0.0444 | -0.0921 | 0.0846 | -0.0827 | 0.1244 | -0.0156 | -0.0265 | 0.184 | -0.0549 | 0.1315 | 20.6765 | 37.8848 | 23.8792 | 18 | 1.8313 | 0.4523 | 0.2481 | 3.9177 | 0.7269 | 5.121 | 0.0682 | -0.4465 | 0.2786 | 0.4617 | -0.0189 | -0.0387 | -0.0231 | 0.0659 | -0.0187 | 0.1856 | -0.0344 | -0.0321 | 0.2746 | -0.1442 | 0.2128 | 28.3506 | 44.6056 | 25.8496 | 19 | 2.4013 | -0.5681 | 1.713 | 1.7292 | -0.8861 | 4.714 | 0.0442 | 0.0926 | 0.1094 | -0.1227 | 0.0274 | -0.0077 | 0.0345 | 0.0431 | -0.108 | 0.1131 | -0.026 | 0.0279 | 0.1406 | 0.0043 | 0.1574 | 26.1169 | 35.6449 | -16.1787 | 20 | 0.4232 | -0.3407 | 0.1909 | 5.058 | -4.0924 | 3.3539 | -0.0552 | 0.0107 | 0.0523 | 0.1011 | 0.0079 | -0.1189 | -0.09 | 0.0695 | 0.0997 | 0.0956 | -0.031 | 0.002 | 0.1449 | -0.0228 | 0.1759 | 31.8676 | 39.4465 | -6.874 | 21 | 0.525 | 0.4399 | -0.2177 | 0.7113 | -0.302 | 0.8683 | 0.021 | -0.0069 | 0.0279 | -0.0346 | -0.0083 | -0.0799 | -0.013 | 0.1084 | -0.0096 | 0.1005 | -0.0102 | -0.0015 | 0.1286 | 0.0009 | 0.1155 | 18.6204 | 32.1112 | -7.9138 | 22 | 1.0023 | 0.483 | -0.2294 | 0.6471 | -0.293 | 1.3184 | 0.0529 | -0.0163 | 0.0135 | 0.0208 | 0.0203 | -0.1281 | -0.1896 | 0.1432 | -0.0468 | 0.1325 | -0.0264 | 0.0051 | 0.1265 | -0.0023 | 0.1494 | 20.0203 | 41.52 | -7.4103 | 23 | 4.0535 | 1.1746 | 0.4235 | 4.8273 | 0.2414 | 2.1623 | 0.0285 | -0.1985 | 0.1569 | 0.1951 | -0.0277 | 0.1346 | -0.1156 | -0.1357 | -0.0035 | 0.0942 | 0.0052 | 0.0085 | 0.1077 | -0.0061 | 0.0731 | 7.6007 | 37.3571 | -5.7761 | 24 | 2.8064 | 0.3976 | 0.2643 | 2.6017 | 0.576 | 1.4303 | 0.0151 | 0.0323 | 0.1915 | -0.0637 | -0.0117 | 0.078 | -0.1202 | -0.0084 | 0.002 | 0.0907 | -0.0015 | 0.0018 | 0.0836 | 0.0184 | 0.0777 | 6.0802 | 37.5084 | -14.4663 | 25 | 3.9363 | -4.3673 | 0.2867 | 6.0453 | -0.9872 | 0.3931 | 0.2282 | 0.2402 | -0.2827 | -0.427 | -0.1293 | 0.3898 | 0.1848 | -0.0997 | -0.0283 | 0.1525 | -0.0192 | -0.0268 | 0.1496 | -0.0054 | 0.1193 | 4.827 | 26.9043 | -24.1096 | 26 | 3.2935 | -2.2662 | -0.2907 | 4.227 | -0.4135 | 0.6486 | -0.0839 | -0.0404 | 0.0271 | 0.0954 | 0.0194 | -0.1811 | -0.0299 | 0.1187 | 0.0412 | 0.1366 | -0.0222 | 0.0056 | 0.1391 | -0.0106 | 0.0841 | 15.2606 | 28.6958 | -19.2761 | 27 | 3.8052 | -3.3103 | 2.0079 | 6.5075 | -3.1439 | 3.8559 | -0.061 | 0.4135 | 0.045 | -0.2379 | 0.0356 | 0.0666 | -0.1309 | -0.1289 | 0.013 | 0.2036 | -0.0407 | 0.0059 | 0.2624 | 0.018 | 0.0712 | 11.8513 | 29.5808 | -31.7001 | 28 | 3.3115 | -0.4949 | 0.669 | 2.2347 | -0.0439 | 2.8318 | -0.027 | 0.2773 | 0.0517 | -0.2118 | 0.0835 | -0.1939 | -0.0873 | 0.0904 | -0.0702 | 0.1394 | -0.0488 | 0.0334 | 0.1366 | 0.0086 | 0.0932 | 21.1396 | 31.6741 | -26.7309 | 29 | 2.6749 | 0.5064 | 1.3788 | 2.4006 | 0.2997 | 3.7912 | 0.0618 | 0.0863 | -0.0988 | 0.0143 | 0.0676 | -0.2726 | 0.1304 | 0.2139 | -0.0808 | 0.132 | -0.0119 | 0.032 | 0.1468 | -0.0084 | 0.1444 | 29.3478 | 32.5581 | -18.6069 | 30 | 5.356 | 0.825 | 0.4046 | 4.1936 | 1.7476 | 6.5022 | -0.026 | 0.6022 | 0.0151 | -0.5225 | 0.1964 | -0.1976 | -0.2084 | 0.1355 | -0.1009 | 0.1766 | -0.0425 | 0.0871 | 0.206 | -0.0128 | 0.1754 | 33.5633 | 35.3148 | -26.2021 |
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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 through 14 )A3 - 14 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 15 through 27 )A15 - 27 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 28 through 69 )A28 - 69 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 70 through 116 )A70 - 116 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 117 through 150 )A117 - 150 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 151 through 171 )A151 - 171 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 172 through 194 )A172 - 194 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 195 through 210 )A195 - 210 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 211 through 225 )A211 - 225 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 3 through 14 )B3 - 14 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 15 through 27 )B15 - 27 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 28 through 69 )B28 - 69 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 70 through 82 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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