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_2356精密化 | PDB_EXTRACT | 3.2 | 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: 2uvd 解像度: 1.65→48.826 Å / SU ML: 0.16 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 17.66
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1749 | 2040 | 1.59 % |
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Rwork | 0.1462 | - | - |
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obs | 0.1467 | 128477 | 99.86 % |
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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: 93.49 Å2 / Biso mean: 23.2 Å2 / Biso min: 9.39 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.65→48.826 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8012 | 0 | 228 | 1006 | 9246 |
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Biso mean | - | - | 27.61 | 34.07 | - |
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残基数 | - | - | - | - | 1064 |
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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_d0.006 | 8737 | X-RAY DIFFRACTION | f_angle_d0.805 | 11949 | X-RAY DIFFRACTION | f_chiral_restr0.052 | 1318 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1561 | X-RAY DIFFRACTION | f_dihedral_angle_d15.41 | 5186 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.6499-1.6883 | 0.2224 | 129 | 0.213 | 8405 | 8534 | 100 | 1.6883-1.7305 | 0.2787 | 134 | 0.202 | 8402 | 8536 | 100 | 1.7305-1.7773 | 0.2325 | 115 | 0.1912 | 8443 | 8558 | 100 | 1.7773-1.8296 | 0.2545 | 134 | 0.1778 | 8391 | 8525 | 100 | 1.8296-1.8887 | 0.1901 | 130 | 0.1701 | 8410 | 8540 | 100 | 1.8887-1.9562 | 0.2159 | 147 | 0.156 | 8438 | 8585 | 100 | 1.9562-2.0345 | 0.2215 | 156 | 0.1566 | 8345 | 8501 | 100 | 2.0345-2.1271 | 0.1455 | 139 | 0.1476 | 8429 | 8568 | 100 | 2.1271-2.2392 | 0.1752 | 137 | 0.1438 | 8395 | 8532 | 100 | 2.2392-2.3795 | 0.1925 | 134 | 0.1414 | 8446 | 8580 | 100 | 2.3795-2.5632 | 0.1796 | 150 | 0.1442 | 8410 | 8560 | 100 | 2.5632-2.8212 | 0.1889 | 128 | 0.1447 | 8460 | 8588 | 100 | 2.8212-3.2293 | 0.1713 | 134 | 0.142 | 8465 | 8599 | 100 | 3.2293-4.0683 | 0.1416 | 136 | 0.1282 | 8470 | 8606 | 100 | 4.0683-48.8475 | 0.1389 | 137 | 0.1311 | 8528 | 8665 | 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 | 2.0056 | 0.3335 | -0.9414 | 1.2448 | -0.445 | 1.1603 | -0.2268 | 0.1373 | -0.2426 | -0.2955 | 0.0751 | 0.1607 | 0.451 | -0.1583 | 0.1419 | 0.2611 | -0.0379 | 0.0307 | 0.1148 | -0.0067 | 0.2169 | 11.4827 | -9.7474 | 21.4553 | 2 | 1.3044 | -0.7382 | -0.0452 | 0.929 | -0.0861 | 0.6768 | -0.0557 | 0.0132 | -0.1562 | 0.0017 | -0.0227 | 0.1584 | 0.1077 | -0.0239 | 0.0689 | 0.1143 | -0.0081 | 0.0086 | 0.1066 | 0.0048 | 0.1496 | 8.4734 | 6.8249 | 28.9051 | 3 | 0.8188 | -0.5912 | -0.3562 | 1.1027 | 0.2064 | 1.1059 | -0.0061 | 0.1433 | -0.1733 | -0.1837 | -0.0774 | 0.2893 | 0.1441 | -0.2692 | 0.0475 | 0.1331 | -0.0421 | -0.0395 | 0.1785 | -0.0184 | 0.1798 | 7.4805 | 11.9602 | 13.4893 | 4 | 2.1419 | 0.8133 | -0.9884 | 2.1252 | 0.4162 | 1.8401 | -0.1697 | -0.4678 | -0.0334 | -0.0984 | 0.0991 | -0.2631 | 0.3209 | 0.6127 | -0.0531 | 0.222 | 0.0541 | 0.0456 | 0.2053 | -0.0206 | 0.1659 | 40.2758 | 10.4396 | 3.794 | 5 | 0.1635 | 0.0884 | -0.0123 | 1.3469 | 1.1065 | 1.9368 | 0.0176 | 0.0195 | 0.0075 | -0.1481 | 0.0508 | -0.1218 | -0.0397 | 0.0836 | -0.0778 | 0.1277 | 0.0024 | 0.0057 | 0.118 | -0.0044 | 0.116 | 30.2767 | 24.7243 | 7.024 | 6 | 0.3324 | 0.0259 | -0.2791 | 1.5583 | 0.6469 | 1.2682 | -0.0414 | -0.1049 | -0.0425 | 0.035 | 0.0604 | -0.2612 | 0.0826 | 0.3392 | -0.0872 | 0.12 | 0.0065 | -0.0008 | 0.193 | 0.016 | 0.1397 | 31.602 | 17.2978 | 22.9907 | 7 | 1.3203 | -0.3661 | -0.7459 | 1.8474 | -1.1386 | 2.7007 | -0.0225 | -0.4305 | 0.0255 | 0.3276 | 0.0668 | 0.1066 | -0.0802 | 0.3337 | -0.0106 | 0.1781 | 0.0287 | 0.0502 | 0.1955 | -0.0164 | 0.1635 | -1.0909 | 35.8985 | 48.4634 | 8 | 1.1048 | -0.6984 | -0.175 | 1.3648 | -0.1323 | 0.4444 | -0.0481 | -0.0332 | -0.0602 | 0.132 | 0.0272 | 0.1901 | -0.024 | -0.0342 | 0.0185 | 0.1075 | 0.0086 | 0.0124 | 0.1238 | 0.0043 | 0.139 | 0.8292 | 22.0684 | 37.663 | 9 | 0.7621 | -0.4706 | -0.3616 | 1.517 | 0.1262 | 0.4041 | -0.0445 | -0.2639 | 0.0025 | 0.2775 | 0.0638 | -0.0842 | -0.0077 | 0.1246 | -0.0265 | 0.1524 | -0.0062 | -0.0119 | 0.1843 | 0.0093 | 0.1107 | 17.3436 | 28.6086 | 38.3207 | 10 | 0.8296 | 0.0783 | -0.789 | 1.2032 | -0.3604 | 2.302 | 0.0848 | 0.0677 | 0.2535 | -0.0729 | 0.0795 | 0.1555 | -0.3294 | -0.1378 | -0.1856 | 0.2173 | 0.0192 | 0.0337 | 0.1185 | 0.0113 | 0.1895 | 15.9765 | 56.7134 | 19.6819 | 11 | 0.4904 | 0.3415 | 0.4263 | 1.4253 | 1.1478 | 1.7091 | 0.0361 | 0.0108 | 0.054 | -0.1405 | 0.0051 | -0.007 | -0.1538 | 0.0375 | -0.0223 | 0.1521 | -0.0016 | 0.0011 | 0.1229 | 0.0096 | 0.1143 | 22.0753 | 41.1733 | 14.2537 | 12 | 0.6655 | -0.0382 | -0.353 | 0.9566 | 0.3348 | 0.7216 | 0.0732 | 0.1228 | 0.0561 | -0.1906 | -0.0472 | 0.1355 | -0.1329 | -0.1635 | -0.0217 | 0.1436 | 0.0199 | -0.0264 | 0.1305 | 0.0188 | 0.1156 | 10.7209 | 35.7228 | 16.3987 |
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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 1 through 81 )A1 - 81 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 82 through 177 )A82 - 177 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 178 through 266 )A178 - 266 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 1 through 66 )B1 - 66 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 67 through 177 )B67 - 177 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 178 through 266 )B178 - 266 | 7 | X-RAY DIFFRACTION | 7 | chain 'C' and (resid 1 through 66 )C1 - 66 | 8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 67 through 177 )C67 - 177 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 178 through 266 )C178 - 266 | 10 | X-RAY DIFFRACTION | 10 | chain 'D' and (resid 1 through 81 )D1 - 81 | 11 | X-RAY DIFFRACTION | 11 | chain 'D' and (resid 82 through 153 )D82 - 153 | 12 | X-RAY DIFFRACTION | 12 | chain 'D' and (resid 154 through 266 )D154 - 266 | | | | | | | | | | | | | | | | | | | | | | | | |
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