ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.9_1692精密化 | PDB_EXTRACT | 3.27 | データ抽出 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHENIX | | 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: 7EEZ 解像度: 1.5→38.119 Å / SU ML: 0.14 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 18.94 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2082 | 2568 | 5.06 % |
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Rwork | 0.1793 | 48198 | - |
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obs | 0.1808 | 50766 | 99.98 % |
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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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原子変位パラメータ | Biso max: 58.26 Å2 / Biso mean: 17.6228 Å2 / Biso min: 5.92 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.5→38.119 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2463 | 0 | 2 | 265 | 2730 |
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Biso mean | - | - | 11.66 | 22.15 | - |
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残基数 | - | - | - | - | 304 |
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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_d0.008 | 2511 | X-RAY DIFFRACTION | f_angle_d1.07 | 3383 | X-RAY DIFFRACTION | f_chiral_restr0.044 | 356 | X-RAY DIFFRACTION | f_plane_restr0.005 | 450 | X-RAY DIFFRACTION | f_dihedral_angle_d13.014 | 949 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork |
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1.5-1.5289 | 0.2404 | 140 | 0.21 | 2635 | 1.5289-1.5601 | 0.2501 | 151 | 0.1988 | 2650 | 1.5601-1.594 | 0.2258 | 143 | 0.1909 | 2618 | 1.594-1.6311 | 0.2121 | 132 | 0.1866 | 2635 | 1.6311-1.6719 | 0.2133 | 153 | 0.1838 | 2665 | 1.6719-1.7171 | 0.2116 | 158 | 0.1731 | 2618 | 1.7171-1.7676 | 0.2124 | 137 | 0.1685 | 2634 | 1.7676-1.8247 | 0.1839 | 117 | 0.1713 | 2660 | 1.8247-1.8899 | 0.1893 | 119 | 0.175 | 2693 | 1.8899-1.9655 | 0.2053 | 129 | 0.1721 | 2666 | 1.9655-2.055 | 0.2159 | 142 | 0.1766 | 2671 | 2.055-2.1633 | 0.1922 | 143 | 0.1753 | 2657 | 2.1633-2.2988 | 0.1964 | 153 | 0.1713 | 2677 | 2.2988-2.4763 | 0.2082 | 163 | 0.1859 | 2656 | 2.4763-2.7254 | 0.221 | 146 | 0.1982 | 2716 | 2.7254-3.1197 | 0.2311 | 144 | 0.1935 | 2719 | 3.1197-3.9298 | 0.2 | 137 | 0.1738 | 2746 | 3.9298-38.119 | 0.1985 | 161 | 0.1679 | 2882 |
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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 | 2.462 | -1.099 | -2.1586 | 4.623 | 1.6274 | 4.9429 | -0.0321 | 0.1481 | 0.5559 | -0.0776 | 0.0498 | 0.3044 | -0.5049 | -0.3963 | -0.0082 | 0.1153 | 0.0194 | 0.0014 | 0.1004 | 0.0305 | 0.1648 | 5.0119 | 27.0558 | 61.9578 | 2 | 2.8771 | -0.0193 | 0.0934 | 2.8516 | -0.6963 | 3.0407 | -0.0965 | -0.0012 | 0.0376 | 0.1422 | 0.1069 | 0.022 | -0.2742 | 0.0143 | -0.0107 | 0.0754 | 0.0109 | -0.0081 | 0.0778 | -0.0226 | 0.0677 | 9.0118 | 23.2915 | 68.2095 | 3 | 4.5181 | 0.882 | -1.7412 | 1.5605 | -0.7831 | 4.1296 | 0.0054 | -0.1961 | 0.365 | 0.084 | -0.0406 | -0.0089 | -0.5747 | 0.429 | -0.0011 | 0.2085 | -0.0617 | -0.0244 | 0.1627 | -0.0393 | 0.1482 | 14.2391 | 31.9297 | 68.9667 | 4 | 1.9112 | 1.9664 | 0.4589 | 3.8975 | 0.8824 | 4.8817 | -0.1981 | 0.0849 | 0.0438 | -0.196 | 0.166 | -0.2412 | -0.3858 | 0.4687 | 0.022 | 0.0934 | -0.0384 | 0.0105 | 0.1216 | -0.0291 | 0.103 | 14.7524 | 26.8552 | 62.7131 | 5 | 0.6046 | 1.2055 | 1.369 | 2.2312 | 2.5251 | 3.438 | -0.0134 | -0.0785 | 0.1786 | -0.0988 | -0.1748 | 0.2674 | -0.0586 | -0.2702 | 0.1641 | 0.0961 | -0.005 | -0.0014 | 0.1109 | 0.0154 | 0.1021 | -0.2946 | 14.9703 | 51.4901 | 6 | 5.4133 | -0.2498 | -0.2073 | 4.1196 | -1.0581 | 6.1306 | -0.0305 | -0.4617 | -0.2952 | 0.5019 | 0.1156 | -0.0747 | 0.5086 | -0.1912 | 0.058 | 0.171 | -0.0166 | -0.0281 | 0.1026 | 0.004 | 0.1027 | 4.4921 | 9.9363 | 66.2815 | 7 | 2.9388 | 0.7011 | 0.4755 | 0.7463 | 1.4674 | 1.6633 | 0.0553 | 0.1379 | -0.1578 | 0.0854 | -0.0312 | 0.0121 | 0.2242 | -0.0771 | -0.025 | 0.101 | -0.0191 | -0.0106 | 0.0622 | 0.0333 | 0.0657 | -1.6817 | 7.0905 | 54.6714 | 8 | 3.9558 | -0.3546 | 3.8101 | 3.933 | 1.7542 | 7.0883 | 0.1337 | -0.0516 | -0.2996 | 0.1836 | 0.2099 | -0.1891 | 0.2948 | 0.2778 | -0.2531 | 0.0838 | 0.0194 | -0.0145 | 0.0811 | 0.0034 | 0.0889 | 8.8812 | 5.8438 | 59.3677 | 9 | 4.3281 | 0.0064 | 0.2481 | 5.6104 | 0.5272 | 1.5961 | 0.059 | -0.1182 | -0.1652 | 0.0892 | -0.0538 | 0.2192 | 0.146 | -0.0483 | -0.0457 | 0.074 | -0.0271 | -0.0143 | 0.115 | 0.006 | 0.0338 | 0.7875 | 8.7709 | 58.3365 | 10 | 5.0725 | 2.4598 | 1.7666 | 4.8847 | 2.1417 | 4.7366 | -0.1783 | 0.2075 | 0.0924 | -0.3205 | 0.0049 | 0.4728 | -0.1244 | -0.35 | 0.2082 | 0.1262 | -0.0117 | -0.0012 | 0.1622 | 0.008 | 0.1256 | -0.7291 | 17.1014 | 43.7091 | 11 | 1.9451 | -1.6691 | -0.0594 | 3.9465 | 1.2928 | 2.885 | 0.0464 | 0.1415 | -0.127 | -0.1242 | -0.1438 | 0.3798 | -0.3389 | -0.4051 | -0.0009 | 0.1567 | 0.0135 | -0.0039 | 0.1503 | -0.0119 | 0.1511 | 5.1893 | 26.4327 | 37.0246 | 12 | 0.978 | -0.0985 | 0.3494 | 2.3927 | -1.142 | 3.3814 | 0.0476 | 0.067 | -0.0486 | -0.0854 | 0.1181 | 0.2085 | 0.0504 | -0.1449 | -0.1604 | 0.0673 | -0.0004 | 0.0008 | 0.081 | 0.0059 | 0.093 | 5.9465 | 17.139 | 31.2238 | 13 | 1.2245 | 1.2529 | 1.4296 | 1.4872 | 2.5204 | 2.847 | -0.0106 | 0.0356 | 0.095 | -0.0797 | 0.0223 | -0.0013 | -0.1524 | 0.1563 | 0.018 | 0.1334 | -0.0386 | -0.0065 | 0.0912 | 0.0255 | 0.1055 | 15.056 | 27.6014 | 41.8577 | 14 | 2.5271 | 0.6871 | -0.1749 | 1.9661 | 0.2764 | 1.4158 | -0.0099 | 0.0934 | 0.1615 | 0.0295 | 0.0678 | -0.1496 | -0.0956 | 0.0527 | -0.0507 | 0.1223 | -0.0341 | -0.0175 | 0.0829 | 0.0189 | 0.1199 | 22.1158 | 34.0871 | 45.9505 | 15 | 6.1628 | -2.4038 | 4.0216 | 4.0812 | -2.7045 | 3.9173 | 0.0377 | -0.62 | -0.3222 | 0.2191 | 0.3056 | 0.0688 | 0.2356 | -0.5316 | -0.4243 | 0.1488 | 0.0099 | 0.0123 | 0.2494 | 0.0037 | 0.1835 | 1.014 | 14.8955 | 70.8983 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 133 through 139 )A133 - 139 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 140 through 152 )A140 - 152 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 153 through 177 )A153 - 177 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 178 through 188 )A178 - 188 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 189 through 205 )A189 - 205 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 206 through 216 )A206 - 216 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 217 through 239 )A217 - 239 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 240 through 250 )A240 - 250 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 251 through 261 )A251 - 261 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 262 through 279 )A262 - 279 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 126 through 145 )B126 - 145 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 146 through 177 )B146 - 177 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 178 through 217 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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