ソフトウェア | 名称 | バージョン | 分類 |
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XSCALE | | データスケーリング | PHENIX | dev_2299精密化 | PDB_EXTRACT | 3.2 | データ抽出 | XDS | | データ削減 | PHASER | | 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: 5HGW 解像度: 1.7→39.012 Å / SU ML: 0.16 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 21.19
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2045 | 1986 | 9.23 % |
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Rwork | 0.1741 | - | - |
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obs | 0.1769 | 21506 | 99.69 % |
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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: 95.55 Å2 / Biso mean: 32.3057 Å2 / Biso min: 12.84 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.7→39.012 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1292 | 0 | 123 | 149 | 1564 |
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Biso mean | - | - | 51.6 | 39.01 | - |
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残基数 | - | - | - | - | 167 |
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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 | 1390 | X-RAY DIFFRACTION | f_angle_d0.846 | 1877 | X-RAY DIFFRACTION | f_chiral_restr0.058 | 201 | X-RAY DIFFRACTION | f_plane_restr0.007 | 245 | X-RAY DIFFRACTION | f_dihedral_angle_d13.559 | 828 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.7-1.7425 | 0.2978 | 130 | 0.2514 | 1376 | 1506 | 99 | 1.7425-1.7896 | 0.2545 | 128 | 0.2392 | 1353 | 1481 | 99 | 1.7896-1.8423 | 0.2719 | 141 | 0.2172 | 1389 | 1530 | 100 | 1.8423-1.9017 | 0.2231 | 117 | 0.2179 | 1385 | 1502 | 100 | 1.9017-1.9697 | 0.232 | 132 | 0.1973 | 1397 | 1529 | 100 | 1.9697-2.0486 | 0.2247 | 131 | 0.1826 | 1369 | 1500 | 100 | 2.0486-2.1418 | 0.2089 | 159 | 0.1693 | 1380 | 1539 | 100 | 2.1418-2.2547 | 0.2167 | 153 | 0.1678 | 1367 | 1520 | 100 | 2.2547-2.396 | 0.1788 | 148 | 0.1789 | 1379 | 1527 | 100 | 2.396-2.5809 | 0.2335 | 136 | 0.1859 | 1401 | 1537 | 100 | 2.5809-2.8406 | 0.2743 | 126 | 0.1777 | 1420 | 1546 | 100 | 2.8406-3.2514 | 0.2109 | 150 | 0.1795 | 1409 | 1559 | 100 | 3.2514-4.0958 | 0.1705 | 159 | 0.1451 | 1397 | 1556 | 100 | 4.0958-39.0221 | 0.179 | 176 | 0.1599 | 1498 | 1674 | 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 | 4.4798 | 1.4382 | 0.5124 | 7.4128 | -4.7607 | 6.2502 | -0.4993 | 0.0288 | -0.6241 | 0.0683 | 0.0476 | -0.2127 | 1.0974 | -0.1547 | -0.0821 | 0.4841 | -0.0301 | 0.1909 | 0.1905 | -0.0107 | 0.3411 | 10.2279 | 79.3353 | 11.0646 | 2 | 1.4575 | 1.1554 | 0.0251 | 2.2239 | -0.795 | 4.7209 | -0.0948 | -0.1385 | -0.406 | -0.0311 | -0.08 | -0.1668 | 0.7524 | -0.0616 | 0.1769 | 0.2426 | 0.0061 | 0.0781 | 0.2231 | 0.0706 | 0.2288 | 8.8808 | 83.8595 | 21.4239 | 3 | 6.2879 | 1.4903 | -0.3525 | 1.0387 | -0.1055 | 1.3946 | 0.0013 | -0.1266 | -0.9329 | -0.4604 | -0.4773 | -0.6543 | 0.4322 | 1.4144 | 0.2449 | 0.578 | 0.1965 | 0.0929 | 0.9593 | 0.1882 | 0.8594 | 29.5494 | 86.0099 | 23.5702 | 4 | 7.1487 | 2.8662 | -1.0452 | 4.22 | -2.3271 | 2.2073 | -0.0349 | -0.2294 | -0.0175 | 0.1317 | 0.0003 | 0.0246 | 0.0393 | 0.136 | 0.1348 | 0.1758 | 0.0145 | 0.0313 | 0.2261 | 0.014 | 0.1216 | 14.3472 | 95.5054 | 25.3236 | 5 | 1.0493 | 0.3398 | 0.159 | 7.5097 | 4.2919 | 4.0963 | -0.1087 | -0.0381 | -0.139 | -0.199 | 0.2659 | -0.449 | 0.1609 | 0.3072 | -0.1859 | 0.205 | 0.0296 | 0.0728 | 0.1805 | 0.017 | 0.1904 | 24.9797 | 93.3626 | 11.69 | 6 | 1.9194 | 1.5557 | -0.2152 | 2.5235 | -0.4782 | 2.9957 | 0.0865 | -0.4304 | -0.2373 | 0.2256 | -0.1018 | -0.1008 | 0.0988 | 0.0204 | 0.0288 | 0.1375 | 0.0418 | 0.0243 | 0.2006 | 0.0565 | 0.1383 | 18.1822 | 93.6783 | 24.8953 | 7 | 4.1411 | -2.6786 | -1.0818 | 4.6439 | 0.9337 | 2.319 | 0.1233 | -0.0049 | -0.0095 | -0.4368 | -0.0105 | -0.2967 | 0.039 | 0.3968 | -0.1163 | 0.2773 | 0.0058 | 0.0722 | 0.2488 | -0.0013 | 0.1763 | 24.1602 | 90.2835 | 3.7666 |
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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 0 through 10 )A0 - 10 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 11 through 61 )A11 - 61 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 62 through 77 )A62 - 77 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 78 through 87 )A78 - 87 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 88 through 112 )A88 - 112 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 113 through 147 )A113 - 147 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 148 through 169 )A148 - 169 | | | | | | | | | | | | | | |
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