ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.20.1_4487: ???)精密化 | HKL-2000 | | データスケーリング | HKL-2000 | | 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: 6X6H 解像度: 2.01→23.22 Å / SU ML: 0.21 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 24.01 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2114 | 1790 | 4.92 % |
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Rwork | 0.1729 | - | - |
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obs | 0.1749 | 36390 | 99.47 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 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: 2.01→23.22 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3840 | 0 | 65 | 181 | 4086 |
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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 | 4008 | X-RAY DIFFRACTION | f_angle_d0.788 | 5429 | X-RAY DIFFRACTION | f_dihedral_angle_d12.74 | 1440 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 633 | X-RAY DIFFRACTION | f_plane_restr0.008 | 692 | | | | | |
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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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2.01-2.07 | 0.3728 | 88 | 0.273 | 2518 | X-RAY DIFFRACTION | 94 | 2.07-2.13 | 0.2901 | 133 | 0.2348 | 2678 | X-RAY DIFFRACTION | 100 | 2.13-2.2 | 0.2752 | 146 | 0.2224 | 2651 | X-RAY DIFFRACTION | 100 | 2.2-2.28 | 0.2531 | 112 | 0.2122 | 2720 | X-RAY DIFFRACTION | 100 | 2.28-2.37 | 0.2489 | 144 | 0.199 | 2627 | X-RAY DIFFRACTION | 100 | 2.37-2.47 | 0.2613 | 165 | 0.1882 | 2652 | X-RAY DIFFRACTION | 100 | 2.48-2.61 | 0.2375 | 116 | 0.1781 | 2700 | X-RAY DIFFRACTION | 100 | 2.61-2.77 | 0.2091 | 132 | 0.1808 | 2673 | X-RAY DIFFRACTION | 100 | 2.77-2.98 | 0.2188 | 133 | 0.1782 | 2674 | X-RAY DIFFRACTION | 100 | 2.98-3.28 | 0.2156 | 155 | 0.1743 | 2658 | X-RAY DIFFRACTION | 100 | 3.28-3.75 | 0.2195 | 151 | 0.156 | 2668 | X-RAY DIFFRACTION | 100 | 3.75-4.72 | 0.1669 | 144 | 0.1347 | 2682 | X-RAY DIFFRACTION | 100 | 4.72-23.22 | 0.1795 | 171 | 0.1686 | 2699 | X-RAY DIFFRACTION | 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 | 3.2908 | -0.4319 | -0.3341 | 0.4319 | 0.2989 | 1.9 | 0.0228 | -0.0071 | 0.4016 | 0.0787 | 0.0238 | -0.1258 | -0.0689 | -0.0079 | -0.0592 | 0.2297 | -0.0294 | -0.0277 | 0.1821 | 0.0147 | 0.2786 | 16.8671 | 41.434 | -0.5446 | 2 | 3.8983 | 0.0529 | -1.9681 | 3.1661 | 0.1145 | 8.9956 | 0.1247 | -0.052 | 0.3457 | 0.1184 | -0.2065 | 0.156 | -0.9776 | -1.0915 | -0.0971 | 0.2526 | 0.0807 | -0.0318 | 0.253 | -0.0377 | 0.3919 | 2.9002 | 46.0291 | 0.9799 | 3 | 3.7265 | 0.3331 | -1.6749 | 3.5427 | 1.0998 | 5.5883 | 0.17 | -0.0045 | -0.0021 | 0.2816 | -0.0297 | -0.6881 | -0.1601 | 0.7268 | -0.1522 | 0.2314 | -0.0494 | -0.038 | 0.2588 | -0.0176 | 0.3239 | 25.8735 | 35.657 | -7.6439 | 4 | 2.4587 | 0.6223 | 0.8759 | 2.6347 | -0.5917 | 3.141 | 0.0298 | 0.263 | -0.0933 | -0.1034 | 0.1365 | 0.1546 | 0.2308 | 0.0267 | -0.1809 | 0.1913 | 0.0295 | -0.0186 | 0.2236 | -0.0134 | 0.2148 | 15.0719 | 29.8051 | -15.8139 | 5 | 7.4231 | -1.9956 | -0.7994 | 4.3309 | -0.0233 | 2.0574 | -0.0096 | -0.5659 | -0.3168 | 0.3413 | 0.0894 | -0.0294 | 0.1687 | 0.0602 | -0.0116 | 0.3432 | -0.0353 | -0.0498 | 0.2416 | 0.0449 | 0.2286 | 13.9856 | 28.3041 | 2.791 | 6 | 8.3107 | -2.0659 | -0.6097 | 6.2277 | -0.1374 | 4.0156 | -0.0034 | -0.4707 | 0.0931 | 0.5978 | 0.1814 | 0.5912 | -0.0828 | -0.5711 | -0.0819 | 0.2581 | -0.0585 | -0.0033 | 0.3902 | 0.0443 | 0.2776 | -4.2265 | 33.9788 | 2.1479 | 7 | 7.1466 | 2.6951 | 0.0434 | 6.7079 | 0.5928 | 7.145 | 0.0598 | -0.4514 | -0.2023 | 0.5303 | 0.0494 | 0.1942 | 0.0347 | -0.6712 | -0.1717 | 0.182 | 0.0093 | -0.0056 | 0.3218 | 0.0128 | 0.2529 | -1.3195 | 34.8237 | 4.9881 | 8 | 5.85 | 2.3142 | 0.81 | 5.9815 | -1.1402 | 4.9071 | 0.2762 | -0.3455 | 0.2162 | 0.024 | -0.1829 | 0.4098 | 0.0226 | -0.3555 | -0.1264 | 0.2021 | 0.0064 | -0.0028 | 0.2067 | -0.0092 | 0.1979 | -27.5531 | 34.9058 | -17.304 | 9 | 4.1472 | -1.2283 | -2.0946 | 4.7973 | 1.0984 | 8.3926 | 0.2485 | 0.3463 | 0.4552 | -0.4629 | 0.0792 | -0.2135 | -0.5649 | 0.3987 | -0.3883 | 0.2313 | -0.0138 | 0.0251 | 0.2424 | 0.0393 | 0.3222 | -15.5996 | 43.5343 | -18.7015 | 10 | 3.7234 | 0.6994 | 0.2906 | 3.9366 | -0.0082 | 4.0478 | 0.1064 | -0.14 | -0.0176 | -0.1175 | 0.1035 | 0.6382 | 0.1796 | -0.6643 | -0.2251 | 0.1967 | -0.0404 | -0.0383 | 0.2857 | 0.0573 | 0.3014 | -30.0724 | 29.2774 | -8.5522 | 11 | 3.0866 | -0.2297 | 0.6847 | 2.6104 | -0.5556 | 3.3423 | 0.1907 | -0.3426 | -0.3458 | 0.0372 | 0.1039 | 0.2255 | 0.3674 | -0.2208 | -0.261 | 0.282 | -0.0865 | -0.0639 | 0.2665 | 0.0571 | 0.2777 | -22.1399 | 22.1941 | -2.502 | 12 | 4.394 | 0.6945 | -0.0999 | 3.7448 | -0.5301 | 4.3222 | 0.2296 | 0.4664 | -0.0913 | -0.3652 | -0.0401 | -0.1771 | 0.4631 | 0.325 | -0.0671 | 0.2997 | 0.0695 | -0.0153 | 0.2265 | -0.0317 | 0.1649 | -12.2824 | 29.4184 | -20.7084 | 13 | 6.6223 | -0.6597 | -1.6803 | 3.5326 | -0.1112 | 8.6336 | 0.0234 | 0.4465 | -0.1827 | -0.273 | -0.2234 | -0.247 | 0.1814 | 0.4402 | -0.0832 | 0.2577 | 0.0287 | 0.0337 | 0.354 | 0.0255 | 0.234 | -8.2033 | 34.3912 | -23.3047 | 14 | 3.5147 | -3.8768 | -3.5786 | 7.5157 | 3.9644 | 3.6458 | 0.5039 | 0.3239 | -0.2063 | -0.5619 | 0.1202 | -1.0389 | -0.4932 | 0.5752 | -0.6626 | 0.3854 | -0.0607 | -0.0038 | 0.3752 | 0.0222 | 0.495 | 12.9664 | 38.1025 | 11.948 | 15 | 5.4286 | 4.554 | 0.9239 | 3.8558 | 0.4925 | 2.4148 | 0.1412 | -0.2201 | 0.3676 | -0.3279 | -0.0307 | 0.9587 | -0.5901 | -0.0208 | -0.1073 | 0.4183 | 0.0325 | -0.0571 | 0.359 | -0.002 | 0.4608 | -22.8373 | 33.3968 | -30.272 |
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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 0 through 27 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 28 through 48 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 49 through 66 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 67 through 164 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 165 through 192 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 193 through 220 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 221 through 241 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 0 through 27 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 28 through 48 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 49 through 76 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 77 through 164 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 165 through 220 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 221 through 241 )14 | X-RAY DIFFRACTION | 14 | chain 'P' and (resid 6 through 11 )15 | X-RAY DIFFRACTION | 15 | chain 'Q' and (resid 6 through 11 ) | | | | | | | | | | | | | | |
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