ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.13 | 精密化 | xia2 | 1 | データスケーリング | PDB_EXTRACT | 1 | データ抽出 | xia2 | 1 | データ削減 | PARROT | 1 | 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: 3PIW 解像度: 1.39→33.15 Å / SU ML: 0.18 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 21.34 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2128 | 1817 | 5.04 % | RANDOM |
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Rwork | 0.1986 | - | - | - |
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obs | 0.1993 | 36077 | 97.86 % | - |
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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 / 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: 1.39→33.15 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1256 | 0 | 14 | 97 | 1367 |
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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 | 1303 | X-RAY DIFFRACTION | f_angle_d0.829 | 1774 | X-RAY DIFFRACTION | f_dihedral_angle_d4.839 | 176 | X-RAY DIFFRACTION | f_chiral_restr0.073 | 196 | X-RAY DIFFRACTION | f_plane_restr0.005 | 230 | | | | | |
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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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1.39-1.43 | 0.3511 | 144 | 0.3288 | 2463 | X-RAY DIFFRACTION | 94 | 1.43-1.47 | 0.3158 | 129 | 0.286 | 2557 | X-RAY DIFFRACTION | 96 | 1.47-1.52 | 0.2479 | 124 | 0.2383 | 2569 | X-RAY DIFFRACTION | 96 | 1.52-1.57 | 0.2321 | 144 | 0.2082 | 2569 | X-RAY DIFFRACTION | 98 | 1.57-1.63 | 0.2164 | 145 | 0.1996 | 2614 | X-RAY DIFFRACTION | 98 | 1.63-1.71 | 0.212 | 143 | 0.2111 | 2609 | X-RAY DIFFRACTION | 98 | 1.71-1.8 | 0.2371 | 116 | 0.2125 | 2628 | X-RAY DIFFRACTION | 98 | 1.8-1.91 | 0.2309 | 151 | 0.204 | 2661 | X-RAY DIFFRACTION | 98 | 1.91-2.06 | 0.2152 | 147 | 0.1945 | 2640 | X-RAY DIFFRACTION | 99 | 2.06-2.27 | 0.1912 | 139 | 0.1811 | 2690 | X-RAY DIFFRACTION | 99 | 2.27-2.59 | 0.2131 | 131 | 0.1884 | 2719 | X-RAY DIFFRACTION | 99 | 2.59-3.27 | 0.1968 | 158 | 0.1983 | 2723 | X-RAY DIFFRACTION | 100 | 3.27-33.15 | 0.2116 | 146 | 0.1949 | 2818 | X-RAY DIFFRACTION | 98 |
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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 | 5.8264 | 1.1959 | -3.4766 | 4.6907 | -1.3518 | 6.7865 | 0.1324 | 0.1558 | 0.1455 | -0.0319 | -0.0363 | -0.2295 | -0.057 | 0.2829 | -0.1485 | 0.1701 | 0.0253 | -0.0195 | 0.1559 | -0.0166 | 0.213 | 25.2466 | 19.0814 | 54.4647 | 2 | 0.8004 | 1.6924 | 0.3547 | 5.1991 | -0.9942 | 3.1629 | -0.0545 | -0.1668 | -0.0725 | 0.5271 | 0.0818 | -0.133 | 0.2316 | 0.2368 | -0.0404 | 0.2248 | 0.0258 | 0.0054 | 0.2212 | 0.0301 | 0.2451 | 15.6118 | 1.6895 | 63.1062 | 3 | 4.8053 | -3.682 | 0.2628 | 4.4609 | 1.0852 | 1.0338 | -1.0721 | -0.9102 | -1.4217 | -0.1961 | 0.0603 | -0.3086 | 1.4348 | 1.1983 | 0.6969 | 0.4659 | 0.1499 | 0.1953 | 0.3993 | 0.0921 | 0.4356 | 34.9864 | 3.4861 | 44.3524 | 4 | 3.4628 | -1.2818 | -3.6509 | 3.4676 | 0.2836 | 4.5295 | -0.0315 | 0.5978 | -0.3261 | -0.2012 | -0.0394 | 0.1769 | 0.1805 | -0.293 | 0.052 | 0.2291 | -0.0036 | -0.0324 | 0.2241 | 0.0092 | 0.17 | 17.2224 | 10.7836 | 47.5671 | 5 | 3.6825 | -0.2196 | -1.437 | 1.7888 | 0.2593 | 4.9858 | 0.1619 | -0.8035 | 0.2885 | 0.7739 | -0.2889 | 0.9412 | 0.1139 | -0.7431 | 0.0675 | 0.4203 | -0.0171 | 0.1461 | 0.3457 | -0.0177 | 0.3707 | 6.2632 | 13.9946 | 66.3608 | 6 | 2.3165 | 0.0105 | -0.3918 | 3.2886 | -0.0372 | 2.485 | 0.0519 | 0.1112 | 0.5913 | 0.0833 | -0.0385 | 0.2688 | -0.6875 | -0.485 | -0.077 | 0.2222 | 0.0362 | -0.0209 | 0.2112 | 0.0119 | 0.2809 | 16.1263 | 21.7103 | 53.5163 | 7 | 4.4814 | 2.1975 | -0.8603 | 3.8937 | -3.3938 | 4.6904 | -0.1387 | 0.859 | -0.7065 | -1.2602 | -0.0275 | 0.2381 | 0.9682 | 0.0001 | 0.2741 | 0.4655 | 0.0567 | -0.0409 | 0.4927 | -0.077 | 0.4468 | 18.476 | 7.9392 | 40.5359 | 8 | 6.8911 | -0.3459 | -0.6703 | 4.7089 | 0.8196 | 6.1166 | -0.0361 | 0.1698 | -0.3269 | 0.2361 | -0.0389 | 0.4507 | 0.1661 | -0.7122 | 0.0816 | 0.1681 | -0.0267 | -0.0174 | 0.2005 | 0.0396 | 0.2422 | 6.5626 | 2.964 | 56.0893 | 9 | 6.2104 | 0.9418 | -2.3579 | 2.8926 | -1.0332 | 3.6682 | -0.0837 | -0.3979 | -0.3618 | 0.1667 | -0.1102 | -0.0458 | 0.1074 | 0.2685 | 0.1834 | 0.1901 | 0.0156 | -0.0028 | 0.1354 | 0.0217 | 0.1431 | 19.9568 | 8.0884 | 59.3228 | 10 | 5.0333 | -1.4833 | -0.4026 | 2.2022 | -1.8348 | 7.494 | -0.0604 | -0.076 | 0.0684 | -0.3954 | -0.2703 | -0.6415 | -0.1911 | 0.349 | 0.3043 | 0.19 | 0.0058 | -0.0145 | 0.236 | 0.0443 | 0.237 | 33.57 | 16.7429 | 49.1775 |
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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 20 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 21 through 42 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 43 through 52 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 53 through 73 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 74 through 86 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 87 through 103 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 104 through 116 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 117 through 132 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 133 through 154 )10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 155 through 162 ) | | | | | | | | | |
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