ソフトウェア | 名称 | 分類 |
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PHENIX | 精密化 | XDS | データ削減 | XDS | データスケーリング | SHELXDE | 位相決定 |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.794→47.771 Å / SU ML: 0.11 / σ(F): 1.94 / 位相誤差: 11.68 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1456 | 21237 | 5 % |
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Rwork | 0.1252 | - | - |
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obs | 0.1263 | 425045 | 99.38 % |
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溶媒の処理 | 減衰半径: 0.7 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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精密化ステップ | サイクル: LAST / 解像度: 1.794→47.771 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 13338 | 0 | 1 | 2119 | 15458 |
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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_d0.008 | 13858 | X-RAY DIFFRACTION | f_angle_d0.9 | 18961 | X-RAY DIFFRACTION | f_dihedral_angle_d10.607 | 8111 | X-RAY DIFFRACTION | f_chiral_restr0.06 | 2144 | X-RAY DIFFRACTION | f_plane_restr0.006 | 2443 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.7939-1.8143 | 0.2065 | 590 | 0.1853 | 11051 | X-RAY DIFFRACTION | 82 | 1.8143-1.8356 | 0.1639 | 716 | 0.1481 | 13569 | X-RAY DIFFRACTION | 100 | 1.8356-1.858 | 0.1608 | 714 | 0.1412 | 13567 | X-RAY DIFFRACTION | 100 | 1.858-1.8815 | 0.1766 | 710 | 0.1414 | 13525 | X-RAY DIFFRACTION | 100 | 1.8815-1.9063 | 0.1553 | 705 | 0.1337 | 13506 | X-RAY DIFFRACTION | 100 | 1.9063-1.9324 | 0.161 | 711 | 0.1306 | 13521 | X-RAY DIFFRACTION | 100 | 1.9324-1.96 | 0.1595 | 717 | 0.1313 | 13562 | X-RAY DIFFRACTION | 100 | 1.96-1.9893 | 0.1465 | 713 | 0.1258 | 13535 | X-RAY DIFFRACTION | 100 | 1.9893-2.0204 | 0.141 | 716 | 0.1202 | 13538 | X-RAY DIFFRACTION | 100 | 2.0204-2.0535 | 0.1427 | 717 | 0.1199 | 13580 | X-RAY DIFFRACTION | 100 | 2.0535-2.0889 | 0.1397 | 711 | 0.1191 | 13444 | X-RAY DIFFRACTION | 100 | 2.0889-2.1269 | 0.1454 | 710 | 0.1197 | 13610 | X-RAY DIFFRACTION | 100 | 2.1269-2.1678 | 0.1376 | 725 | 0.1156 | 13572 | X-RAY DIFFRACTION | 100 | 2.1678-2.212 | 0.135 | 707 | 0.1149 | 13544 | X-RAY DIFFRACTION | 100 | 2.212-2.2601 | 0.131 | 706 | 0.1071 | 13480 | X-RAY DIFFRACTION | 100 | 2.2601-2.3127 | 0.136 | 711 | 0.1102 | 13572 | X-RAY DIFFRACTION | 100 | 2.3127-2.3705 | 0.1492 | 713 | 0.1156 | 13546 | X-RAY DIFFRACTION | 100 | 2.3705-2.4346 | 0.1372 | 709 | 0.1128 | 13570 | X-RAY DIFFRACTION | 100 | 2.4346-2.5063 | 0.1393 | 716 | 0.111 | 13510 | X-RAY DIFFRACTION | 100 | 2.5063-2.5872 | 0.1239 | 720 | 0.1078 | 13606 | X-RAY DIFFRACTION | 100 | 2.5872-2.6796 | 0.1294 | 712 | 0.1089 | 13459 | X-RAY DIFFRACTION | 100 | 2.6796-2.7869 | 0.138 | 712 | 0.1145 | 13531 | X-RAY DIFFRACTION | 100 | 2.7869-2.9137 | 0.1415 | 718 | 0.1178 | 13581 | X-RAY DIFFRACTION | 100 | 2.9137-3.0673 | 0.1481 | 714 | 0.1202 | 13525 | X-RAY DIFFRACTION | 100 | 3.0673-3.2594 | 0.1496 | 711 | 0.1238 | 13555 | X-RAY DIFFRACTION | 100 | 3.2594-3.511 | 0.1498 | 716 | 0.1338 | 13563 | X-RAY DIFFRACTION | 100 | 3.511-3.8642 | 0.1559 | 696 | 0.13 | 13552 | X-RAY DIFFRACTION | 100 | 3.8642-4.423 | 0.1359 | 712 | 0.1197 | 13545 | X-RAY DIFFRACTION | 100 | 4.423-5.5712 | 0.1238 | 708 | 0.1159 | 13542 | X-RAY DIFFRACTION | 100 | 5.5712-47.7883 | 0.1837 | 701 | 0.1855 | 13547 | X-RAY DIFFRACTION | 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 | 0.897 | -1.0682 | -0.0562 | 2.8065 | -0.506 | 1.5562 | -0.0218 | 0.1093 | -0.5477 | -0.3122 | 0.0478 | 0.0766 | 0.5605 | -0.2077 | -0.0122 | 0.4984 | -0.0929 | -0.0755 | 0.2179 | -0.0889 | 0.4967 | 8.8586 | 48.4515 | 85.2426 | 2 | 0.3933 | 0.0304 | 0.0363 | 0.5194 | -0.0646 | 0.295 | 0.0029 | -0.0409 | -0.1197 | -0.0532 | 0.0276 | 0.0616 | 0.0769 | -0.0763 | -0.0275 | 0.1108 | -0.0326 | -0.0209 | 0.1417 | 0.0274 | 0.1121 | 3.9549 | 86.1006 | 103.3755 | 3 | 0.9144 | 0.2908 | 0.0197 | 1.1992 | 0.6139 | 0.8763 | -0.0126 | 0.0784 | 0.1878 | -0.1608 | -0.0028 | 0.0586 | -0.1767 | -0.0616 | 0.0274 | 0.1434 | 0.029 | -0.011 | 0.1544 | -0.0105 | 0.1233 | 16.1731 | 140.6996 | 124.9699 | 4 | 2.6899 | 1.2633 | 0.5526 | 2.1453 | 0.3861 | 1.8063 | 0.0322 | 0.3462 | -0.594 | -0.3537 | 0.0088 | 0.0219 | 0.5158 | -0.0549 | -0.0382 | 0.5062 | 0.0154 | 0.0145 | 0.1998 | -0.1323 | 0.4693 | 27.7406 | 50.3764 | 79.6072 | 5 | 0.4354 | -0.029 | -0.0534 | 0.5821 | 0.1364 | 0.5931 | 0.0144 | 0.0302 | -0.0472 | -0.0967 | 0.002 | -0.0432 | 0.0153 | 0.0204 | -0.0177 | 0.1106 | -0.0025 | 0.0121 | 0.1181 | 0.0087 | 0.0841 | 31.64 | 92.5221 | 93.3462 | 6 | 0.9181 | 0.0032 | 0.038 | 1.2354 | 0.4617 | 1.0556 | 0.0391 | 0.0521 | 0.2239 | -0.1058 | 0.0251 | -0.1378 | -0.2029 | 0.1339 | -0.0724 | 0.146 | -0.021 | 0.0319 | 0.1527 | -0.0348 | 0.1729 | 31.358 | 144.3602 | 130.7208 | 7 | 1.5319 | -0.0717 | -0.182 | 1.0744 | -0.3922 | 1.5362 | -0.0351 | 0.1397 | -0.5438 | -0.1816 | -0.0158 | -0.0812 | 0.5978 | 0.0422 | 0.0457 | 0.4451 | 0.0193 | -0.0038 | 0.155 | -0.0277 | 0.5147 | 27.2608 | 43.8897 | 96.9406 | 8 | 0.5244 | -0.1367 | -0.0203 | 0.5597 | 0.0278 | 0.2598 | -0.0156 | -0.1624 | -0.1113 | 0.0564 | 0.0126 | 0.003 | 0.0594 | 0.0125 | 0.0062 | 0.1251 | -0.0049 | -0.0108 | 0.1703 | 0.0582 | 0.1217 | 27.9531 | 82.1334 | 121.4607 | 9 | 0.8166 | -0.0529 | -0.0518 | 0.8459 | 0.3499 | 0.8651 | 0.0268 | -0.0988 | 0.16 | 0.0292 | -0.0089 | -0.0256 | -0.111 | -0.0293 | -0.0049 | 0.1088 | 0.0033 | 0.0031 | 0.1313 | -0.052 | 0.1402 | 20.0404 | 140.5727 | 139.8535 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 16 through 55 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 56 through 442 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 443 through 602 )4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 16 through 55 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 56 through 471 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 472 through 602 )7 | X-RAY DIFFRACTION | 7 | chain 'C' and (resid 16 through 79 )8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 80 through 472 )9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 473 through 602 ) | | | | | | | | |
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