ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | SHELXD | | 位相決定 | MLPHARE | | 位相決定 | 直接法 | | モデル構築 | ARP | | モデル構築 | WARP | | モデル構築 | HKL-3000 | | 位相決定 | PHENIX | (phenix.refine: 1.8.1_1168)精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | 直接法 | | 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: 1.936→47.839 Å / σ(F): 0 / 位相誤差: 24.59 / 立体化学のターゲット値: TWIN_LSQ_F
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2238 | 2037 | 4.18 % | random |
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Rwork | 0.1726 | - | - | - |
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all | 0.1784 | 48781 | - | - |
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obs | 0.1784 | 48781 | 90.64 % | - |
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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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精密化ステップ | サイクル: LAST / 解像度: 1.936→47.839 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4920 | 0 | 27 | 510 | 5457 |
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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 | 5111 | X-RAY DIFFRACTION | f_angle_d1.178 | 6986 | X-RAY DIFFRACTION | f_dihedral_angle_d15.208 | 1927 | X-RAY DIFFRACTION | f_chiral_restr0.067 | 795 | X-RAY DIFFRACTION | f_plane_restr0.007 | 924 | | | | | |
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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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1.939-1.9875 | 0.3084 | 62 | 0.2603 | 1478 | X-RAY DIFFRACTION | 39 | 1.9875-2.0413 | 0.273 | 108 | 0.2444 | 2481 | X-RAY DIFFRACTION | 66 | 2.0413-2.1013 | 0.2621 | 135 | 0.2362 | 3032 | X-RAY DIFFRACTION | 79 | 2.1013-2.1691 | 0.3096 | 142 | 0.2216 | 3359 | X-RAY DIFFRACTION | 89 | 2.1691-2.2467 | 0.2484 | 151 | 0.2076 | 3596 | X-RAY DIFFRACTION | 94 | 2.2467-2.3366 | 0.227 | 153 | 0.2004 | 3624 | X-RAY DIFFRACTION | 95 | 2.3366-2.443 | 0.307 | 153 | 0.1896 | 3638 | X-RAY DIFFRACTION | 96 | 2.443-2.5718 | 0.2182 | 153 | 0.1978 | 3620 | X-RAY DIFFRACTION | 96 | 2.5718-2.7329 | 0.2575 | 152 | 0.1859 | 3690 | X-RAY DIFFRACTION | 96 | 2.7329-2.9438 | 0.2377 | 157 | 0.1772 | 3670 | X-RAY DIFFRACTION | 96 | 2.9438-3.24 | 0.1917 | 156 | 0.1631 | 3660 | X-RAY DIFFRACTION | 96 | 3.24-3.7087 | 0.1881 | 159 | 0.1411 | 3662 | X-RAY DIFFRACTION | 95 | 3.7087-4.672 | 0.1774 | 156 | 0.1262 | 3605 | X-RAY DIFFRACTION | 94 | 4.672-47.8535 | 0.2888 | 154 | 0.1669 | 3659 | X-RAY DIFFRACTION | 93 |
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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 | 1.1783 | -0.3824 | -0.3377 | 1.867 | 0.2243 | 0.7052 | -0.0535 | 0.0542 | 0.1321 | 0.0619 | -0.0703 | 0.1753 | -0.3218 | -0.3386 | 0.1336 | 0.0833 | 0.0026 | 0.0319 | 0.0401 | 0.0085 | 0.1305 | 30.2209 | 24.9263 | 80.5847 | 2 | 1.7939 | 0.2558 | -0.2075 | 2.2879 | 1.2963 | 0.8576 | 0.2894 | -0.4914 | 0.6661 | 0.3485 | -0.1129 | 0.0769 | -0.3113 | -0.1767 | -0.1401 | 0.2513 | 0.0176 | 0.1004 | 0.1701 | -0.0702 | 0.3548 | 29.5286 | 33.2658 | 89.5698 | 3 | 1.8005 | -0.051 | -0.0038 | 0.6429 | -0.2885 | 1.0661 | 0.0674 | 0.0086 | 0.0826 | 0.0868 | -0.0544 | 0.0998 | -0.0745 | -0.1489 | 0.0237 | 0.0708 | -0.0135 | -0.0057 | 0.0677 | -0.0155 | 0.0609 | 33.9699 | 20.0884 | 85.1666 | 4 | 3.069 | 0.2136 | -0.4254 | 3.363 | 1.6868 | 3.0697 | -0.05 | 0.0083 | 0.1394 | 0.2557 | -0.2798 | 0.3649 | 0.0583 | -0.5112 | 0.1476 | 0.1056 | -0.0033 | 0.0242 | 0.1315 | -0.0215 | 0.2712 | 18.8148 | 25.9144 | 83.48 | 5 | 1.2332 | 0.2801 | -0.1254 | 1.1136 | 0.1786 | 1.2587 | 0.0583 | 0.1769 | 0.5419 | -0.1436 | -0.141 | 0.1176 | -0.3049 | -0.1646 | -0.0316 | 0.1793 | 0.0433 | 0.0127 | 0.1097 | 0.0459 | 0.2366 | 32.7252 | 33.9346 | 75.0941 | 6 | 2.0655 | -0.5207 | -0.0498 | 2.2381 | 0.2471 | 1.4965 | 0.1031 | -0.02 | -0.3609 | 0.2202 | -0.0664 | -0.0294 | 0.1908 | 0.2408 | 0.0075 | 0.0707 | 0.0119 | -0.0352 | 0.088 | -0.0259 | 0.1416 | 53.6154 | 3.1309 | 83.284 | 7 | 1.4695 | 0.0958 | -1.6478 | 1.5731 | 1.8822 | 4.3723 | -0.1098 | -0.0211 | -0.1072 | 0.3462 | -0.025 | -0.3275 | 0.0977 | 0.0316 | -0.1139 | 0.1004 | 0.0289 | 0.0264 | -0.0826 | -0.0181 | 0.193 | 50.7405 | 21.0356 | 92.042 | 8 | 0.0701 | -0.1545 | 0.022 | 0.8311 | 0.2013 | 0.3768 | 0.0753 | -0.0055 | 0.0742 | -0.0854 | 0.0056 | -0.1769 | 0.0163 | 0.0931 | 0.1834 | 0.0667 | 0.0183 | -0.0139 | -0.0811 | 0.0741 | 0.1372 | 56.1864 | 14.6843 | 81.5889 | 9 | 2.4446 | 1.7112 | -2.189 | 2.3453 | -1.0763 | 3.0063 | -0.0801 | -0.1279 | -0.1524 | 0.1638 | 0.0059 | 0.0899 | 0.2717 | 0.0006 | 0.0543 | 0.1059 | 0.0362 | -0.0161 | 0.0291 | 0.0122 | 0.1425 | 42.3127 | 5.44 | 86.7511 | 10 | 2.5301 | 2.3968 | -2.6815 | 5.6803 | -6.4193 | 9.2342 | 0.3136 | -0.3263 | -0.0736 | 0.3299 | -0.3619 | -0.233 | -0.4665 | 0.5737 | 0.1267 | 0.1657 | 0.0003 | -0.0362 | 0.2414 | -0.0258 | 0.1989 | 64.4492 | 5.2649 | 83.5409 | 11 | 1.4225 | -0.6966 | -0.4836 | 0.905 | -0.0827 | 1.1107 | 0.1148 | 0.2429 | -0.5444 | -0.0787 | -0.0348 | 0.2783 | 0.4967 | 0.0561 | 0.1341 | 0.1858 | 0.047 | -0.0371 | 0.1151 | -0.0823 | 0.2182 | 50.4839 | -2.5077 | 75.4352 | 12 | 0.6882 | 0.1345 | 0.3601 | 0.9391 | 0.3439 | 2.0287 | -0.0303 | 0.3437 | 0.2335 | -0.2533 | -0.2452 | -0.0251 | -0.1791 | 0.3028 | -0.2135 | 0.1887 | -0.0263 | 0.0381 | 0.2835 | 0.19 | 0.0939 | 52.045 | 25.941 | 60.9601 | 13 | 1.0782 | -0.4498 | -0.5232 | 0.6961 | -0.2071 | 0.6107 | -0.0159 | 0.636 | 0.5472 | -0.7688 | -0.028 | 0.1929 | -0.4541 | 0.0418 | -0.0596 | 0.6044 | -0.0007 | 0.0089 | 0.4182 | 0.2531 | 0.2567 | 52.3669 | 34.5731 | 51.8712 | 14 | 0.3608 | 0.4262 | 0.4635 | 0.71 | 0.2957 | 0.9368 | 0.0151 | 0.6392 | 0.0116 | -0.302 | -0.0013 | -0.2213 | -0.1606 | 0.1873 | 0.067 | 0.2091 | 0.0818 | 0.0234 | 0.3495 | 0.0739 | 0.0312 | 48.8309 | 20.5482 | 56.0915 | 15 | 2.0768 | -0.9334 | -0.4731 | 3.2295 | -1.5701 | 2.8178 | 0.0013 | 0.4537 | 0.332 | -0.3837 | -0.1083 | -0.2225 | -0.2196 | 0.4882 | 0.0411 | 0.2784 | -0.0709 | 0.0073 | 0.4889 | 0.188 | 0.3071 | 59.5709 | 32.1322 | 62.6456 | 16 | 0.6805 | 0.8825 | -0.3056 | 1.6638 | -1.2463 | 2.0602 | -0.0195 | 0.2395 | 0.4398 | -0.1094 | -0.2188 | -0.1074 | -0.4792 | 0.1083 | 0.0208 | 0.2432 | 0.0638 | 0.013 | 0.1866 | 0.1263 | 0.2185 | 46.0468 | 34.1493 | 65.882 | 17 | 0.3163 | -0.0314 | -0.2579 | 0.6249 | -0.3487 | 2.0248 | -0.0262 | 0.5783 | -0.2155 | -0.1563 | -0.0363 | 0.0879 | 0.0798 | -0.2745 | 0.0616 | 0.1368 | 0.0382 | -0.0635 | 0.4133 | -0.1069 | 0.1541 | 30.6767 | 5.3516 | 61.766 | 18 | 3.3194 | 1.0523 | 1.8307 | 5.2359 | 0.5479 | 2.0201 | 0.2637 | 0.5656 | -0.7571 | -0.4019 | 0.0575 | -0.1276 | 0.4581 | -0.2986 | -0.4939 | 0.281 | -0.0493 | -0.0892 | 0.7477 | -0.2203 | 0.311 | 30.9088 | -3.1379 | 51.7992 | 19 | 0.6554 | 0.1145 | -0.2885 | 1.1837 | -0.8754 | 0.9401 | 0.017 | 0.361 | -0.0219 | -0.3245 | 0.0404 | 0.1377 | 0.1919 | -0.1844 | 0.0716 | 0.2409 | 0.0305 | -0.1162 | 0.4904 | -0.0768 | 0.0986 | 28.1027 | 15.4547 | 53.539 | 20 | 0.5927 | 0.2701 | 0.2796 | 0.793 | -0.3574 | 0.5575 | 0.0204 | 0.3948 | -0.16 | -0.3126 | -0.0642 | 0.0913 | 0.1434 | -0.1943 | 0.0762 | 0.2287 | 0.064 | -0.0523 | 0.4006 | -0.1105 | 0.0804 | 37.6166 | 8.1356 | 57.6616 | 21 | 0.5519 | 0.4378 | 0.2289 | 0.8205 | 0.3638 | 1.1238 | 0.0201 | 0.548 | -0.389 | -0.0938 | -0.0316 | 0.1016 | 0.3625 | -0.3755 | -0.1141 | 0.2413 | -0.0343 | -0.0413 | 0.3849 | -0.1458 | 0.2367 | 30.031 | -1.2856 | 63.1735 | 22 | 3.2481 | -1.3847 | -0.604 | 4.4712 | -0.4237 | 4.6256 | 0.089 | -0.1128 | -0.6206 | 0.5216 | -0.0903 | 0.1249 | 0.6616 | -0.0706 | 0.0922 | 0.2366 | -0.047 | -0.113 | 0.1611 | -0.0072 | 0.2501 | 36.8634 | -2.2322 | 75.7362 |
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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 32 through 62 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 63 through 76 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 77 through 139 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 140 through 151 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 152 through 191 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 33 through 76 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 77 through 82 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 83 through 110 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 111 through 139 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 140 through 151 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 152 through 190 )12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 32 through 62 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 63 through 76 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 77 through 139 )15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resid 140 through 163 )16 | X-RAY DIFFRACTION | 16 | chain 'C' | | | | | | | | | | | | | | | |
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