ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.21rc1_5177: ???)精密化 | Aimless | | データスケーリング | 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 / 解像度: 1.9→45.45 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.48 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.236 | 1249 | 4.95 % |
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Rwork | 0.2166 | - | - |
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obs | 0.2176 | 25255 | 99.25 % |
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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: 1.9→45.45 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2398 | 0 | 1 | 83 | 2482 |
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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_d0.004 | 2438 | X-RAY DIFFRACTION | f_angle_d0.7 | 3290 | X-RAY DIFFRACTION | f_dihedral_angle_d11.25 | 880 | X-RAY DIFFRACTION | f_chiral_restr0.057 | 383 | X-RAY DIFFRACTION | f_plane_restr0.005 | 423 | | | | | |
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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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1.9-1.98 | 0.4181 | 178 | 0.3317 | 2549 | X-RAY DIFFRACTION | 98 | 1.98-2.07 | 0.3221 | 118 | 0.2645 | 2617 | X-RAY DIFFRACTION | 98 | 2.07-2.17 | 0.3255 | 137 | 0.2669 | 2617 | X-RAY DIFFRACTION | 99 | 2.17-2.31 | 0.2421 | 114 | 0.2512 | 2659 | X-RAY DIFFRACTION | 99 | 2.31-2.49 | 0.3014 | 124 | 0.2558 | 2679 | X-RAY DIFFRACTION | 100 | 2.49-2.74 | 0.3278 | 131 | 0.2536 | 2678 | X-RAY DIFFRACTION | 100 | 2.74-3.14 | 0.2552 | 129 | 0.2394 | 2689 | X-RAY DIFFRACTION | 100 | 3.14-3.95 | 0.2176 | 153 | 0.2053 | 2713 | X-RAY DIFFRACTION | 100 | 3.95-45.45 | 0.188 | 165 | 0.1777 | 2805 | 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 | 4.8034 | -3.2022 | -5.6769 | 4.5186 | 4.7162 | 7.0718 | 0.6201 | -0.5076 | -0.5679 | 1.3645 | -0.8106 | -1.6948 | -0.3126 | 4.1602 | -0.0281 | 0.8315 | -0.0404 | -0.169 | 1.1636 | 0.1676 | 0.744 | 9.7562 | -6.6366 | 16.7788 | 2 | 4.6329 | 4.2569 | -1.6244 | 6.1323 | -0.1541 | 4.8179 | 0.0794 | 0.2996 | 0.302 | -0.9504 | 0.0357 | 0.5902 | 0.1553 | -0.8592 | -0.0009 | 0.3967 | 0.1299 | -0.0086 | 0.4027 | 0.02 | 0.2861 | -11.9919 | -4.1763 | 9.2299 | 3 | 9.4171 | 0.1459 | 5.1823 | 8.1613 | -0.0043 | 2.8695 | -0.5242 | 0.6675 | 1.3259 | -0.7422 | -0.2621 | 0.1402 | -1.5197 | -0.0292 | 0.6674 | 0.4674 | -0.0011 | 0.0428 | 0.2663 | 0.044 | 0.3403 | -4.4847 | 5.2739 | 9.8397 | 4 | 2.8415 | 3.9866 | 0.6042 | 9.4043 | 0.2067 | 3.8396 | -0.1149 | -0.0291 | 0.5031 | 0.5048 | -0.0793 | -0.0534 | -0.0764 | 0.2182 | 0.0569 | 0.404 | -0.0016 | -0.0087 | 0.3746 | 0.0236 | 0.3454 | 0.5215 | -0.0631 | 13.4967 | 5 | 3.456 | -0.5983 | -4.0844 | 9.7332 | 1.6444 | 4.9468 | 0.1166 | -0.5178 | 0.1872 | -0.5928 | 0.0399 | 0.4415 | -0.1215 | -1.6636 | -0.1247 | 0.2868 | 0.0274 | -0.0245 | 0.8146 | -0.0026 | 0.3304 | -22.1487 | -8.4594 | 14.2102 | 6 | 3.7504 | 2.4464 | -1.214 | 2.6705 | -0.5115 | 0.4889 | -0.2104 | -1.2091 | -0.3244 | 0.0877 | -0.0923 | -0.0658 | -0.7154 | -0.095 | 0.3577 | 0.6925 | 0.0485 | 0.0177 | 0.5761 | -0.0014 | 0.3086 | -5.3676 | -2.5847 | 22.2381 | 7 | 5.7749 | 2.3743 | -2.7691 | 5.3721 | -6.1624 | 7.0933 | 0.302 | -1.1878 | 2.0524 | 0.2629 | 0.2813 | -0.2876 | -2.2417 | -0.7976 | -0.3459 | 1.0911 | 0.257 | -0.003 | 0.5659 | -0.1168 | 0.7303 | -11.907 | 6.7993 | 17.3735 | 8 | 5.7039 | 2.795 | 2.494 | 2.6254 | 1.823 | 6.2325 | 0.2594 | -0.2047 | 0.7364 | -0.0121 | -0.2173 | 0.48 | -0.6897 | -0.9161 | -0.028 | 0.5496 | 0.2406 | 0.0459 | 0.6561 | -0.0475 | 0.3779 | -14.0327 | -1.1802 | 19.8293 | 9 | 8.238 | 3.9841 | 2.4755 | 6.113 | 3.5595 | 2.079 | -0.3886 | 0.5773 | 0.6889 | -0.7817 | -0.5199 | 0.0767 | -1.1007 | 1.0818 | 0.5105 | 0.6365 | -0.1373 | -0.0625 | 0.6008 | 0.2015 | 0.3133 | 11.3006 | -1.9 | 37.2659 | 10 | 2.3694 | -3.2732 | -0.8248 | 4.8296 | -0.0114 | 3.969 | 0.3774 | -0.6314 | -0.4441 | -0.6066 | 0.4105 | 0.2794 | 0.2683 | -1.1143 | -0.5778 | 0.4385 | -0.1837 | -0.068 | 0.8325 | 0.1017 | 0.2996 | -21.2609 | -18.2401 | 17.1279 | 11 | 2.877 | -2.1089 | -0.3121 | 5.8606 | 3.4186 | 7.7772 | 0.1953 | -0.4635 | -0.1239 | -0.3331 | 0.0983 | 0.1296 | 0.7892 | -1.3029 | 0.0967 | 0.6401 | -0.1149 | -0.0385 | 0.6181 | -0.0317 | 0.2674 | -14.9119 | -19.8295 | 15.5115 | 12 | 8.0472 | -4.8079 | -2.9786 | 5.0861 | 5.62 | 7.8153 | -0.0843 | -0.6144 | 0.2297 | -0.2485 | 0.8175 | -0.3808 | 0.1039 | -0.8839 | -0.2831 | 0.5975 | -0.1048 | -0.0233 | 0.4877 | 0.0136 | 0.2386 | -13.0197 | -18.2528 | 25.2642 | 13 | 2.1646 | -3.1889 | -0.4611 | 4.6601 | 0.6871 | 0.1017 | 0.404 | -1.3448 | -0.4456 | 1.4198 | -0.4415 | 0.6616 | 0.6357 | -0.4068 | -0.0409 | 1.2139 | -0.7442 | -0.226 | 1.3784 | 0.2364 | 0.5932 | -21.005 | -27.669 | 22.5285 | 14 | 5.5667 | 2.8925 | 3.3681 | 5.2152 | 4.0522 | 3.5088 | -0.0632 | -0.3364 | -0.3809 | -0.5232 | 0.2346 | 0.2033 | 0.4708 | -0.628 | -0.1401 | 1.0461 | -0.2978 | -0.0615 | 0.4803 | 0.0421 | 0.3794 | -12.9301 | -26.3283 | 20.3083 | 15 | 3.1937 | 2.438 | -2.965 | 6.6827 | -1.6106 | 3.1786 | -0.0448 | -0.1518 | 0.2468 | -0.769 | -0.0021 | 0.7596 | 0.4247 | -1.0443 | 0.1783 | 0.5325 | -0.0618 | -0.0854 | 0.5567 | -0.0126 | 0.403 | -9.5655 | -12.0032 | 45.9404 | 16 | 3.1273 | 1.0331 | 0.1801 | 5.5134 | -0.626 | 3.2433 | 0.0286 | 0.0684 | -0.4315 | 0.1172 | -0.1243 | -0.3253 | 0.7134 | 0.3359 | 0.1083 | 0.5546 | 0.0771 | 0.0128 | 0.2903 | -0.0036 | 0.2649 | 0.5437 | -19.7971 | 9.8302 | 17 | 7.0421 | 1.521 | -3.9633 | 5.0064 | -3.5963 | 4.7244 | -0.1825 | -0.2809 | 0.0146 | -0.3229 | -0.7286 | -1.6415 | 1.0245 | 1.403 | 0.3031 | 0.7729 | 0.2977 | -0.0043 | 0.8679 | -0.0794 | 0.478 | 9.8924 | -19.7872 | 6.8014 | 18 | 4.5979 | 1.7026 | 1.9916 | 6.5885 | 0.1727 | 3.7012 | -0.0504 | 0.4915 | -0.268 | -0.3056 | 0.0266 | -0.2503 | 0.8564 | 0.5684 | 0.0948 | 0.3824 | 0.1221 | 0.0259 | 0.3953 | 0.0234 | 0.293 | 6.4871 | -12.9941 | 11.72 | 19 | 5.3888 | -5.2996 | 6.8927 | 5.5043 | -6.9372 | 8.9855 | 1.0577 | 0.9442 | -0.3833 | -0.0539 | -0.7519 | -0.1152 | 1.3117 | 1.4424 | -0.3964 | 1.049 | 0.171 | -0.0817 | 0.5413 | -0.0425 | 0.379 | 7.7584 | -25.4157 | 37.4798 |
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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 -3 through 1 ) | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 2 through 16 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 17 through 30 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 31 through 43 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 44 through 57 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 58 through 74 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 75 through 87 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 88 through 102 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 103 through 113 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 0 through 31 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 32 through 57 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 58 through 72 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 73 through 88 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 89 through 102 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 103 through 112 )16 | X-RAY DIFFRACTION | 16 | chain 'C' and (resid 0 through 75 )17 | X-RAY DIFFRACTION | 17 | chain 'C' | | | | | | | | | | | | | | | |
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