ソフトウェア | 名称 | バージョン | 分類 |
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StructureStudio | | データ収集 | PHENIX | (phenix.refine: 1.6.1_357)精密化 | d*TREK | | データ削減 | d*TREK | | データスケーリング | |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: PDB entry 3NAA 解像度: 1.6→29.175 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic with TLS / 交差検証法: THROUGHOUT / σ(F): 1.34 / σ(I): -3 / 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 | 0.2245 | 3214 | 5.35 % | random |
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Rwork | 0.2004 | - | - | - |
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obs | 0.2017 | 60044 | 89.15 % | - |
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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 / Bsol: 59.515 Å2 / ksol: 0.423 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.9106 Å2 | -0 Å2 | -2.5506 Å2 |
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2- | - | 3.346 Å2 | -0 Å2 |
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3- | - | - | -0.4354 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→29.175 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3357 | 0 | 18 | 620 | 3995 |
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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 | 3499 | X-RAY DIFFRACTION | f_angle_d1.095 | 4759 | X-RAY DIFFRACTION | f_dihedral_angle_d12.621 | 1258 | X-RAY DIFFRACTION | f_chiral_restr0.077 | 531 | X-RAY DIFFRACTION | f_plane_restr0.005 | 607 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection obs | % reflection obs (%) |
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1.6-1.6217 | 0.2259 | 68 | 0.2161 | 1203 | 1203 | 44 | 1.6217-1.647 | 0.2522 | 103 | 0.2177 | 1643 | 1643 | 60 | 1.647-1.674 | 0.2641 | 112 | 0.2117 | 2028 | 2028 | 73 | 1.674-1.7029 | 0.2263 | 128 | 0.1952 | 2312 | 2312 | 84 | 1.7029-1.7338 | 0.2027 | 128 | 0.1951 | 2402 | 2402 | 87 | 1.7338-1.7672 | 0.2215 | 146 | 0.1927 | 2463 | 2463 | 89 | 1.7672-1.8032 | 0.2353 | 140 | 0.1928 | 2487 | 2487 | 91 | 1.8032-1.8424 | 0.2082 | 135 | 0.1891 | 2540 | 2540 | 92 | 1.8424-1.8853 | 0.2218 | 147 | 0.1911 | 2598 | 2598 | 94 | 1.8853-1.9324 | 0.2008 | 150 | 0.1871 | 2643 | 2643 | 96 | 1.9324-1.9847 | 0.2243 | 159 | 0.1852 | 2723 | 2723 | 97 | 1.9847-2.043 | 0.1987 | 139 | 0.1773 | 2725 | 2725 | 99 | 2.043-2.109 | 0.1925 | 147 | 0.1751 | 2789 | 2789 | 100 | 2.109-2.1843 | 0.1967 | 161 | 0.1679 | 2759 | 2759 | 100 | 2.1843-2.2717 | 0.1891 | 162 | 0.1699 | 2748 | 2748 | 100 | 2.2717-2.3751 | 0.2007 | 163 | 0.1745 | 2774 | 2774 | 100 | 2.3751-2.5002 | 0.2062 | 135 | 0.181 | 2779 | 2779 | 100 | 2.5002-2.6568 | 0.2276 | 154 | 0.1822 | 2756 | 2756 | 100 | 2.6568-2.8618 | 0.1973 | 162 | 0.1767 | 2781 | 2781 | 100 | 2.8618-3.1495 | 0.1836 | 160 | 0.1807 | 2735 | 2735 | 99 | 3.1495-3.6045 | 0.2186 | 157 | 0.172 | 2548 | 2548 | 92 | 3.6045-4.5385 | 0.1991 | 134 | 0.198 | 2194 | 2194 | 78 | 4.5385-29.1796 | 0.2311 | 124 | 0.2177 | 2200 | 2200 | 77 |
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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 | 0.8755 | 0.3795 | 0.2176 | 0.1696 | 0.1723 | 0.5217 | 0.1615 | -0.0582 | -0.558 | 0.2163 | 0.0663 | -0.1656 | 0.2834 | -0.0238 | -0.1596 | 0.24 | 0.0078 | -0.0608 | 0.1727 | 0.0005 | 0.2942 | 24.5066 | -15.0378 | 29.9647 | 2 | 0.3239 | 0.258 | 0.51 | 0.313 | 0.185 | 1.4041 | 0.2984 | -0.6158 | -0.252 | 0.1186 | -0.1554 | 0.0168 | 0.1021 | -0.6182 | -0.1899 | 0.2103 | -0.0725 | -0.0206 | 0.3424 | 0.0952 | 0.1702 | 10.8294 | -10.6148 | 33.5543 | 3 | 1.3546 | 0.8476 | 0.5755 | 0.6891 | 0.351 | 0.385 | 0.1992 | -0.3685 | -0.0754 | 0.2143 | -0.1914 | -0.0486 | 0.129 | -0.2834 | -0.0151 | 0.22 | -0.0548 | -0.0029 | 0.2809 | 0.0518 | 0.1365 | 24.0792 | -4.5218 | 39.4766 | 4 | 0.4252 | 0.3089 | 0.4647 | 0.4842 | 0.293 | 0.7624 | 0.1875 | -0.2793 | -0.2011 | 0.1381 | -0.0928 | -0.045 | 0.0441 | -0.1408 | -0.064 | 0.1882 | -0.0446 | -0.0114 | 0.2441 | 0.0558 | 0.1434 | 22.8057 | -6.7574 | 34.722 | 5 | 0.8829 | 0.17 | 0.6263 | 0.5998 | -0.4087 | 0.8611 | -0.0032 | 0.0703 | -0.0293 | -0.2057 | 0.079 | 0.1511 | 0.1981 | -0.0369 | -0.0599 | 0.1505 | 0.0039 | -0.0034 | 0.1025 | -0.0004 | 0.1222 | 2.7904 | -2.9983 | 0.381 | 6 | 0.7675 | -0.1023 | 0.036 | 0.601 | -0.2573 | 0.1913 | 0.0463 | 0.5821 | 0.1451 | -0.1468 | -0.0209 | -0.1738 | -0.3346 | -0.058 | -0.0388 | 0.2256 | -0.0346 | 0.0293 | 0.2509 | 0.0356 | 0.1576 | 12.1025 | -0.3814 | -8.0107 | 7 | 0.7958 | 0.227 | 0.0673 | 0.2756 | 0.1193 | 0.2222 | 0.0595 | -0.1039 | -0.0449 | -0.0296 | 0.0113 | -0.0766 | -0.0387 | 0.0438 | -0.0522 | 0.115 | 0.0071 | 0.0167 | 0.0978 | -0.0006 | 0.1306 | 10.023 | -5.6447 | 7.6202 | 8 | 0.2751 | -0.2923 | 0.0707 | 0.5994 | 0.1098 | 0.1897 | 0.2435 | 0.3484 | 0.07 | -0.776 | -0.1779 | 0.0521 | 0.6094 | 0.3229 | -0.0874 | 0.5015 | -0.0105 | -0.0036 | 0.3535 | -0.0488 | 0.125 | 13.1526 | -6.7424 | -13.7305 | 9 | 0.4119 | 0.1026 | 0.1086 | 0.6281 | 0.2563 | 0.7604 | 0.0195 | 0.0206 | -0.1689 | -0.1007 | 0.1245 | 0.0236 | 0.1521 | 0.0526 | -0.1775 | 0.2013 | 0.0016 | 0.0008 | 0.075 | 0.0015 | 0.1813 | 6.0429 | -13.7666 | 3.5613 | 10 | 0.6417 | 0.5291 | -0.9107 | 2.6923 | 0.8163 | 2.4409 | 0.3813 | -0.0657 | -0.181 | 0.2956 | -0.1393 | -0.181 | 0.7895 | -1.1539 | -0.1458 | 0.3023 | -0.1155 | -0.0745 | 0.3392 | 0.0329 | 0.2496 | -2.8789 | -2.8383 | -11.247 | 11 | 0.6425 | -0.1382 | -0.1457 | 0.5227 | -0.2986 | 1.3778 | 0.0792 | 0.0509 | 0.1448 | 0.1498 | 0.1497 | -0.0269 | -0.461 | -0.2673 | -0.1586 | 0.2208 | 0.0475 | 0.0092 | 0.1913 | 0.0078 | 0.1628 | 30.7222 | 12.124 | 24.5366 | 12 | 0.7744 | -0.1373 | -0.2966 | 0.5426 | -0.0316 | 1.6798 | -0.073 | 0.1274 | 0.0391 | 0.1414 | -0.1573 | 0.0825 | -0.4092 | -0.0451 | 0.1714 | 0.2194 | -0.0348 | -0.0014 | 0.1318 | -0.0003 | 0.1582 | 38.2742 | 11.1209 | 21.3505 | 13 | 0.5157 | 0.3404 | 0.3573 | 0.7766 | -0.173 | 1.545 | 0.0823 | -0.1439 | -0.0835 | 0.0466 | -0.0872 | -0.1151 | 0.0218 | -0.4528 | 0.022 | 0.1506 | -0.0393 | -0.0061 | 0.1585 | -0.0044 | 0.122 | 35.1822 | 3.5274 | 28.881 | 14 | 1.7005 | 0.1514 | 0.0463 | 1.813 | 0.2617 | 1.0176 | -0.2171 | 0.1889 | 0.1478 | 0.1444 | 0.3523 | -0.0636 | 0.1807 | -0.0223 | -0.0714 | 0.168 | -0.0427 | 0.0024 | 0.1559 | 0.0234 | 0.1477 | 33.3959 | -4.5289 | 24.7623 | 15 | 0.5478 | 0.1361 | -0.2389 | 0.4187 | -0.06 | 1.0739 | -0.0127 | -0.006 | 0.0257 | 0.0682 | -0.0615 | -0.0822 | -0.1292 | 0.0632 | 0.061 | 0.1502 | -0.0096 | -0.0011 | 0.1462 | 0.0024 | 0.1398 | 37.9916 | 4.1666 | 25.642 | 16 | 0.1433 | -0.218 | 0.1926 | 0.3276 | -0.4329 | 0.8481 | -0.0271 | 0.2439 | 0.0301 | -0.0759 | 0.0097 | 0.0204 | 0.0868 | 0.1701 | 0.0079 | 0.1088 | 0.0013 | 0.0177 | 0.1119 | -0.0053 | 0.113 | 14.1503 | 4.6302 | -1.0391 | 17 | 0.609 | -0.4915 | 0.3093 | 0.3525 | -0.3309 | 0.2592 | -0.1014 | 0.0444 | 0.2155 | -0.0044 | 0.0739 | 0.0516 | 0.0339 | 0.0873 | 0.0172 | 0.0818 | 0.0022 | 0.0077 | 0.1128 | -0.0058 | 0.1274 | 12.9654 | 6.8847 | 2.6924 | 18 | 0.6024 | 0.0933 | 0.1703 | 0.7758 | 0.1429 | 0.4872 | -0.1358 | 0.0117 | 0.1761 | 0.0557 | 0.137 | -0.006 | -0.2004 | 0.1636 | -0.0287 | 0.1133 | 0.0125 | -0.007 | 0.1037 | -0.0147 | 0.1494 | 4.8928 | 15.0444 | 4.1128 | 19 | 0.4533 | 0.1175 | -0.0441 | 0.1066 | -0.0093 | 0.0853 | -0.0227 | -0.0067 | -0.0249 | -0.0105 | 0.0335 | 0.0188 | -0.0587 | 0.0772 | -0.0131 | 0.1008 | 0.0046 | 0.0093 | 0.1088 | 0.0102 | 0.125 | 8.9813 | 6.9951 | 2.1459 | 20 | 1.244 | -0.0861 | 0.8747 | 0.7495 | -0.1379 | 0.7199 | -0.0327 | 0.2178 | 0.5911 | -0.0279 | -0.1702 | 0.0348 | -0.0377 | 0.1201 | 0.137 | 0.1204 | -0.0198 | -0.0076 | 0.1088 | 0.0459 | 0.2203 | 10.2969 | 13.4846 | -6.0042 |
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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 H and resid 1:10)2 | X-RAY DIFFRACTION | 2 | (chain H and resid 11:23)3 | X-RAY DIFFRACTION | 3 | (chain H and resid 24:71)4 | X-RAY DIFFRACTION | 4 | (chain H and resid 72:113)5 | X-RAY DIFFRACTION | 5 | (chain H and resid 114:131)6 | X-RAY DIFFRACTION | 6 | (chain H and resid 132:141)7 | X-RAY DIFFRACTION | 7 | (chain H and resid 142:182)8 | X-RAY DIFFRACTION | 8 | (chain H and resid 183:192)9 | X-RAY DIFFRACTION | 9 | (chain H and resid 193:211)10 | X-RAY DIFFRACTION | 10 | (chain H and resid 212:217)11 | X-RAY DIFFRACTION | 11 | (chain L and resid 1:13)12 | X-RAY DIFFRACTION | 12 | (chain L and resid 14:27)13 | X-RAY DIFFRACTION | 13 | (chain L and resid 28:41)14 | X-RAY DIFFRACTION | 14 | (chain L and resid 42:47)15 | X-RAY DIFFRACTION | 15 | (chain L and resid 48:104)16 | X-RAY DIFFRACTION | 16 | (chain L and resid 105:125)17 | X-RAY DIFFRACTION | 17 | (chain L and resid 126:145)18 | X-RAY DIFFRACTION | 18 | (chain L and | | | | | | | | | | | | | | | | | |
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