ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.14 | 精密化 | PROTEUM PLUS | | データ削減 | PROTEUM PLUS | | データスケーリング | 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: 2.191→26.864 Å / SU ML: 0.26 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 24.18 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2422 | 3832 | 6.47 % |
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Rwork | 0.1951 | - | - |
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obs | 0.1981 | 28750 | 98.67 % |
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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: 2.191→26.864 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4724 | 0 | 18 | 196 | 4938 |
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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_d0.002 | 4848 | X-RAY DIFFRACTION | f_angle_d0.553 | 6575 | X-RAY DIFFRACTION | f_dihedral_angle_d9.27 | 2890 | X-RAY DIFFRACTION | f_chiral_restr0.038 | 711 | X-RAY DIFFRACTION | f_plane_restr0.004 | 872 | | | | | |
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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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2.191-2.2186 | 0.3315 | 125 | 0.3037 | 1774 | X-RAY DIFFRACTION | 85 | 2.2186-2.2478 | 0.3204 | 145 | 0.2791 | 2042 | X-RAY DIFFRACTION | 99 | 2.2478-2.2785 | 0.3539 | 140 | 0.2752 | 2099 | X-RAY DIFFRACTION | 99 | 2.2785-2.3111 | 0.2811 | 142 | 0.262 | 1996 | X-RAY DIFFRACTION | 99 | 2.3111-2.3455 | 0.3151 | 145 | 0.2568 | 2079 | X-RAY DIFFRACTION | 99 | 2.3455-2.3822 | 0.2762 | 148 | 0.2584 | 2071 | X-RAY DIFFRACTION | 99 | 2.3822-2.4212 | 0.3517 | 142 | 0.2637 | 2075 | X-RAY DIFFRACTION | 99 | 2.4212-2.4629 | 0.2684 | 138 | 0.2458 | 2039 | X-RAY DIFFRACTION | 99 | 2.4629-2.5077 | 0.2959 | 144 | 0.2409 | 2099 | X-RAY DIFFRACTION | 99 | 2.5077-2.5559 | 0.2665 | 143 | 0.2312 | 2031 | X-RAY DIFFRACTION | 99 | 2.5559-2.608 | 0.3087 | 139 | 0.2321 | 2026 | X-RAY DIFFRACTION | 99 | 2.608-2.6647 | 0.3106 | 143 | 0.2166 | 2070 | X-RAY DIFFRACTION | 99 | 2.6647-2.7266 | 0.2783 | 147 | 0.2213 | 2054 | X-RAY DIFFRACTION | 99 | 2.7266-2.7947 | 0.2753 | 141 | 0.2225 | 2095 | X-RAY DIFFRACTION | 99 | 2.7947-2.8702 | 0.2202 | 139 | 0.218 | 2026 | X-RAY DIFFRACTION | 99 | 2.8702-2.9545 | 0.2696 | 145 | 0.2128 | 2071 | X-RAY DIFFRACTION | 99 | 2.9545-3.0498 | 0.3073 | 142 | 0.2224 | 2070 | X-RAY DIFFRACTION | 99 | 3.0498-3.1586 | 0.2375 | 150 | 0.2077 | 2097 | X-RAY DIFFRACTION | 99 | 3.1586-3.2849 | 0.2728 | 141 | 0.2044 | 2017 | X-RAY DIFFRACTION | 99 | 3.2849-3.4341 | 0.2634 | 141 | 0.1874 | 2090 | X-RAY DIFFRACTION | 100 | 3.4341-3.6147 | 0.2187 | 147 | 0.1776 | 2042 | X-RAY DIFFRACTION | 99 | 3.6147-3.8406 | 0.2149 | 138 | 0.1656 | 2082 | X-RAY DIFFRACTION | 100 | 3.8406-4.1362 | 0.2174 | 144 | 0.1491 | 2067 | X-RAY DIFFRACTION | 99 | 4.1362-4.5506 | 0.1739 | 137 | 0.1369 | 2059 | X-RAY DIFFRACTION | 99 | 4.5506-5.2049 | 0.1829 | 143 | 0.1447 | 2090 | X-RAY DIFFRACTION | 100 | 5.2049-6.542 | 0.1996 | 140 | 0.1719 | 2066 | X-RAY DIFFRACTION | 100 | 6.542-26.864 | 0.1421 | 143 | 0.1397 | 2051 | 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 | 1.9199 | -0.8412 | 1.1622 | 0.7191 | -0.1716 | 1.4174 | -0.1016 | 0.0174 | 0.492 | 0.0121 | -0.2 | -0.097 | -0.5121 | -0.1241 | 0.0709 | 0.2548 | 0.0992 | -0.0302 | 0.1714 | -0.042 | 0.2481 | -5.8605 | 19.6932 | -11.801 | 2 | 0.2011 | -0.0047 | 0.1541 | 0.2234 | 0.0879 | 2.6511 | 0.0076 | -0.0014 | 0.027 | -0.0511 | 0.0129 | -0.0081 | 0.001 | -0.3115 | -0.0239 | 0.128 | 0.0455 | 0.0097 | 0.1309 | 0.0119 | 0.1618 | -6.2073 | 5.4573 | -27.176 | 3 | 2.8302 | -0.5458 | 0.8815 | 1.4668 | 0.3829 | 1.2353 | -0.2667 | -0.2843 | 0.0886 | 0.2858 | 0.1765 | -0.2288 | -0.176 | -0.1401 | 0.026 | 0.2757 | 0.159 | -0.0375 | 0.3482 | -0.0752 | 0.2434 | 26.0929 | -7.7964 | -11.3328 | 4 | 0.9923 | -0.8464 | 0.362 | 2.1855 | 0.6062 | 1.266 | -0.1446 | -0.0233 | 1.0885 | -0.0701 | -0.0192 | -0.3596 | -0.4546 | 0.0967 | -0.0468 | 0.4088 | 0.1659 | -0.1186 | 0.4843 | -0.0789 | 0.6327 | 32.8534 | -0.7494 | -11.8037 | 5 | 0.9436 | -0.5953 | 0.6785 | 0.5105 | -0.269 | 0.662 | -0.1832 | -0.3794 | 0.6357 | 0.3007 | 0.1095 | -0.507 | -0.0747 | 0.0873 | -0.0119 | 0.2855 | 0.1192 | -0.0806 | 0.3679 | -0.128 | 0.4819 | 28.2998 | -2.2174 | -10.3007 | 6 | 1.7318 | 0.0019 | 0.3424 | 0.4029 | -0.2127 | 0.2277 | -0.0329 | 0.083 | 0.1295 | -0.0551 | 0.02 | -0.3771 | 0.0219 | 0.1042 | 0.0148 | 0.1477 | 0.3048 | -0.0305 | 0.3168 | -0.0907 | 0.3097 | 37.1532 | -14.1521 | -17.6 | 7 | 1.4603 | -0.3682 | 0.2501 | 0.3815 | 0.0549 | 0.8969 | 0.0438 | -0.1134 | -0.0238 | 0.07 | -0.0056 | -0.0621 | 0.2435 | 0.0571 | 0.1477 | 0.2649 | 0.2068 | -0.0194 | 0.2645 | -0.0164 | 0.1895 | 31.4675 | -19.1272 | -17.885 | 8 | 1.7801 | -1.1804 | 0.5174 | 1.4332 | -0.1585 | 1.2734 | -0.0897 | -0.2129 | 0.1329 | -0.1241 | 0.0442 | -0.1433 | 0.2062 | 0.1286 | 0.0506 | 0.1708 | 0.0846 | 0.0383 | 0.2388 | 0.0188 | 0.2252 | 23.6105 | -13.2442 | -17.6555 | 9 | 0.9833 | -0.1318 | 0.1057 | 0.4334 | 0.1532 | 1.9042 | -0.0322 | -0.2878 | -0.2342 | 0.1566 | 0.1625 | 0.1851 | 0.2572 | -0.246 | -0.0878 | 0.2581 | 0.0817 | 0.0414 | 0.2682 | 0.0643 | 0.2194 | 21.1293 | -21.3499 | -19.4389 | 10 | 1.0678 | -0.6861 | 0.2565 | 1.803 | -0.4961 | 1.4101 | -0.1043 | -0.1007 | -0.2289 | 0.1697 | 0.2935 | 0.2997 | 0.1871 | -0.3457 | -0.1199 | 0.2098 | -0.0048 | 0.003 | 0.2046 | 0.0419 | 0.1783 | 13.9893 | -19.649 | -35.7855 | 11 | 1.6949 | -0.7557 | -0.6315 | 0.7505 | 0.4903 | 0.4632 | -0.3968 | -0.2406 | 0.4241 | 0.1104 | 0.3954 | -0.1859 | -0.3892 | -0.1026 | -0.007 | 0.3938 | 0.0306 | -0.1015 | 0.2426 | -0.0065 | 0.2525 | 26.4763 | -8.5582 | -33.5429 | 12 | 1.6181 | -0.4319 | 0.3525 | 1.285 | -0.1488 | 2.1457 | -0.1151 | 0.1751 | -0.1311 | 0.2133 | 0.2523 | -0.1879 | 0.2011 | 0.4023 | -0.0497 | 0.1835 | 0.0533 | -0.0251 | 0.25 | -0.0223 | 0.1401 | 29.5174 | -22.1648 | -41.1552 |
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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 'B' and (resid 4 through 82 )2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 83 through 314 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 6 through 27 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 28 through 45 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 46 through 75 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 76 through 96 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 97 through 137 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 138 through 161 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 162 through 209 )10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 210 through 259 )11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 260 through 283 )12 | X-RAY DIFFRACTION | 12 | chain 'A' and (resid 284 through 314 ) | | | | | | | | | | | |
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