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 | XDS | | データ削減 | XSCALE | | 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 開始モデル: 2CPL 解像度: 1.294→47.874 Å / SU ML: 0.15 / 交差検証法: FREE R-VALUE / σ(F): 1.99 / 位相誤差: 20.75 / 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 | 0.1949 | 2461 | 2.01 % | Random selection |
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Rwork | 0.1694 | - | - | - |
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obs | 0.1699 | 122350 | 97.11 % | - |
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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: 1.294→47.874 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4228 | 0 | 4 | 1147 | 5379 |
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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 | 4418 | X-RAY DIFFRACTION | f_angle_d1.219 | 6000 | X-RAY DIFFRACTION | f_dihedral_angle_d12.218 | 1680 | X-RAY DIFFRACTION | f_chiral_restr0.048 | 647 | X-RAY DIFFRACTION | f_plane_restr0.006 | 801 | | | | | |
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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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1.2942-1.319 | 0.3525 | 97 | 0.3387 | 5692 | X-RAY DIFFRACTION | 83 | 1.319-1.346 | 0.2849 | 128 | 0.2819 | 6755 | X-RAY DIFFRACTION | 99 | 1.346-1.3752 | 0.3041 | 148 | 0.2746 | 6675 | X-RAY DIFFRACTION | 98 | 1.3752-1.4072 | 0.2497 | 146 | 0.2494 | 6698 | X-RAY DIFFRACTION | 98 | 1.4072-1.4424 | 0.2546 | 129 | 0.2293 | 6702 | X-RAY DIFFRACTION | 98 | 1.4424-1.4814 | 0.2334 | 139 | 0.2101 | 6789 | X-RAY DIFFRACTION | 99 | 1.4814-1.525 | 0.2056 | 143 | 0.1909 | 6698 | X-RAY DIFFRACTION | 98 | 1.525-1.5743 | 0.2347 | 127 | 0.1836 | 6749 | X-RAY DIFFRACTION | 99 | 1.5743-1.6305 | 0.1662 | 141 | 0.1649 | 6759 | X-RAY DIFFRACTION | 99 | 1.6305-1.6958 | 0.1981 | 144 | 0.164 | 6703 | X-RAY DIFFRACTION | 98 | 1.6958-1.773 | 0.1941 | 139 | 0.1614 | 6807 | X-RAY DIFFRACTION | 99 | 1.773-1.8665 | 0.202 | 145 | 0.1592 | 6751 | X-RAY DIFFRACTION | 99 | 1.8665-1.9834 | 0.1793 | 141 | 0.1599 | 6632 | X-RAY DIFFRACTION | 97 | 1.9834-2.1366 | 0.1926 | 141 | 0.1515 | 6606 | X-RAY DIFFRACTION | 96 | 2.1366-2.3516 | 0.2058 | 133 | 0.1536 | 6741 | X-RAY DIFFRACTION | 98 | 2.3516-2.6918 | 0.1719 | 163 | 0.154 | 6717 | X-RAY DIFFRACTION | 98 | 2.6918-3.3913 | 0.1587 | 126 | 0.1526 | 6630 | X-RAY DIFFRACTION | 96 | 3.3913-47.9072 | 0.1783 | 131 | 0.1485 | 6785 | X-RAY DIFFRACTION | 97 |
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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 | 1.6714 | -1.4235 | 0.5093 | 1.7709 | -0.3687 | 0.6574 | -0.0076 | 0.0743 | 0.1624 | -0.0237 | -0.0264 | -0.1605 | -0.0729 | 0.0326 | 0.068 | 0.0957 | -0.0115 | 0.0008 | 0.1056 | -0.0054 | 0.1328 | 8.7191 | 17.8729 | 42.943 | 2 | 0.8625 | -0.2348 | 0.3388 | 0.7763 | 0.1361 | 1.0442 | -0.0103 | -0.0427 | -0.0246 | 0.0641 | -0.0011 | 0.0157 | 0.0157 | -0.0359 | -0.0205 | 0.0705 | -0.0058 | 0.0116 | 0.0745 | 0.0094 | 0.0811 | 11.9873 | -0.5086 | 48.9736 | 3 | 3.0055 | -0.8552 | -0.2567 | 0.5874 | 0.0408 | 0.3421 | -0.0614 | -0.0883 | 0.0085 | 0.0476 | 0.041 | 0.0592 | 0.0203 | -0.0531 | 0.0101 | 0.0941 | -0.0168 | 0.0041 | 0.0781 | -0.0111 | 0.0968 | -5.9126 | 2.3268 | 50.2229 | 4 | 1.5476 | -0.1877 | 0.272 | 0.419 | 0.1486 | 0.5972 | -0.0107 | -0.0026 | -0.134 | 0.03 | 0.0119 | 0.0461 | 0.0246 | 0.0052 | 0.0084 | 0.0773 | -0.0016 | 0.0158 | 0.057 | 0.0124 | 0.0927 | 8.7633 | -2.0411 | 45.0559 | 5 | 2.2339 | -0.754 | 0.6012 | 1.1896 | -0.2635 | 1.3681 | 0.0328 | 0.1822 | -0.159 | -0.0564 | -0.0225 | 0.0146 | -0.01 | 0.0836 | -0.007 | 0.0772 | 0.0048 | 0.0115 | 0.0651 | 0.0018 | 0.0956 | 2.0877 | 15.1777 | 37.8512 | 6 | 2.4716 | 0.2543 | 0.233 | 3.689 | 1.2983 | 3.8163 | -0.1696 | 0.1952 | -0.3518 | -0.1855 | 0.0223 | 0.1994 | 0.2305 | -0.1942 | 0.1409 | 0.1137 | -0.0223 | 0.0214 | 0.1213 | 0.0061 | 0.1623 | 11.874 | -22.1157 | 78.2078 | 7 | 1.5765 | -0.1337 | 0.1681 | 0.5596 | -0.1413 | 0.6855 | -0.0104 | -0.0879 | 0.1085 | 0.0378 | -0.0001 | 0.0247 | -0.0409 | -0.0202 | -0.0014 | 0.0804 | 0.0058 | 0.0201 | 0.073 | -0.0024 | 0.0838 | 5.8526 | 2.6253 | 88.0184 | 8 | 3.8278 | 0.313 | 1.2275 | 1.0518 | 0.5826 | 0.9177 | -0.0167 | 0.0252 | -0.1748 | -0.0074 | 0.0231 | -0.0737 | 0.0647 | 0.1053 | -0.0087 | 0.0878 | 0.0052 | 0.0207 | 0.0805 | 0.0087 | 0.1258 | 31.8801 | -6.2523 | 85.2645 | 9 | 1.1355 | -0.0356 | -0.0892 | 0.6503 | -0.1532 | 0.5595 | -0.0198 | 0.0178 | 0.075 | -0.0043 | 0.0297 | 0.0044 | -0.0302 | -0.0361 | -0.0167 | 0.0863 | 0.0044 | 0.011 | 0.0691 | 0.0023 | 0.0982 | 9.6011 | 2.8799 | 82.154 | 10 | 1.4219 | -0.2359 | -0.4203 | 1.2327 | -0.0093 | 0.8526 | -0.0267 | 0.1416 | -0.094 | -0.0868 | 0.0066 | -0.0578 | 0.0298 | -0.0568 | 0.0252 | 0.1078 | 0.0041 | 0.0071 | 0.0885 | -0.0245 | 0.1152 | 16.0268 | -14.5357 | 75.2794 |
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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 0 through 28 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 29 through 70 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 71 through 145 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 146 through 224 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 225 through 266 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 1 through 19 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 20 through 95 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 96 through 145 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 146 through 224 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 225 through 266 ) | | | | | | | | | |
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