ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | HKL-3000 | | データ収集 | HKL-3000 | | 位相決定 | MOLREP | | 位相決定 | PHENIX | (phenix.refine: 1.7_650)精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDBID 1U6Z 解像度: 1.8→30.191 Å / SU ML: 0.2 / Isotropic thermal model: mixed / 交差検証法: THROUGHOUT / σ(F): 0 / 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 | 0.228 | 2033 | 5.04 % | random |
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Rwork | 0.177 | - | - | - |
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all | 0.179 | 40375 | - | - |
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obs | 0.179 | 40375 | 96.95 % | - |
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溶媒の処理 | 減衰半径: 0.95 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 41.119 Å2 / ksol: 0.303 e/Å3 |
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原子変位パラメータ | Biso mean: 28.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 10.4832 Å2 | 0 Å2 | -6.3566 Å2 |
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2- | - | -4.247 Å2 | 0 Å2 |
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3- | - | - | -6.2362 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.8→30.191 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3320 | 0 | 11 | 466 | 3797 |
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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_d0.011 | 3740 | X-RAY DIFFRACTION | f_angle_d1.366 | 5113 | X-RAY DIFFRACTION | f_dihedral_angle_d15.007 | 1450 | X-RAY DIFFRACTION | f_chiral_restr0.106 | 553 | X-RAY DIFFRACTION | f_plane_restr0.009 | 681 | | | | | |
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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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1.8001-1.842 | 0.3227 | 141 | 0.2651 | 2498 | 2639 | 96 | 1.842-1.888 | 0.2978 | 136 | 0.2373 | 2623 | 2759 | 99 | 1.888-1.9391 | 0.2892 | 126 | 0.2073 | 2604 | 2730 | 99 | 1.9391-1.9961 | 0.278 | 144 | 0.2027 | 2593 | 2737 | 99 | 1.9961-2.0605 | 0.2473 | 126 | 0.1898 | 2600 | 2726 | 99 | 2.0605-2.1341 | 0.2445 | 157 | 0.1721 | 2566 | 2723 | 99 | 2.1341-2.2196 | 0.2279 | 137 | 0.1756 | 2608 | 2745 | 99 | 2.2196-2.3206 | 0.2442 | 126 | 0.1696 | 2577 | 2703 | 99 | 2.3206-2.4428 | 0.2256 | 147 | 0.1723 | 2585 | 2732 | 98 | 2.4428-2.5958 | 0.2259 | 153 | 0.1711 | 2582 | 2735 | 98 | 2.5958-2.7961 | 0.2508 | 130 | 0.1693 | 2570 | 2700 | 98 | 2.7961-3.0772 | 0.2273 | 131 | 0.1757 | 2544 | 2675 | 97 | 3.0772-3.5219 | 0.2097 | 118 | 0.1608 | 2482 | 2600 | 93 | 3.5219-4.435 | 0.1892 | 130 | 0.1534 | 2466 | 2596 | 92 | 4.435-30.1951 | 0.2082 | 131 | 0.1866 | 2444 | 2575 | 91 |
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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 | 2.1037 | 0.249 | 1.6532 | 1.2449 | 0.4424 | 1.8925 | -0.0939 | -0.3659 | 0.0896 | 0.1818 | -0.0096 | -0.0341 | -0.2327 | -0.4116 | 0.0939 | 0.1851 | 0.0432 | 0.0032 | 0.1365 | -0.0025 | 0.1243 | 15.2383 | 18.3365 | 2.0274 | 2 | 0.1696 | -0.3131 | -0.2931 | 0.9607 | -0.4232 | 0.879 | -0.0634 | -0.0073 | -0.0037 | 0.1622 | 0.025 | 0.1007 | -0.2402 | -0.0938 | -0.0059 | 0.0532 | 0.0007 | 0.0262 | 0.0596 | -0.0021 | 0.0497 | 17.8877 | 4.1486 | 10.6544 | 3 | 0.1069 | 0.2652 | 0.0957 | 0.7878 | -0.1545 | 0.3655 | 0.0264 | 0.0798 | -0.0035 | 0.0936 | -0.033 | -0.0095 | 0.0137 | -0.0195 | -0.0041 | 0.0544 | -0.0046 | 0.013 | 0.0906 | 0.0026 | 0.0578 | 18.971 | 9.0295 | -7.1921 | 4 | 0.4749 | 0.3567 | 0.6065 | 1.1913 | 0.1499 | 0.3332 | -0.2315 | 0.3919 | -0.1515 | -0.0965 | 0.1376 | -0.2427 | -0.0073 | 0.1976 | 0.0114 | 0.0687 | 0.0071 | 0.0091 | 0.1127 | 0.0133 | 0.0919 | 28.9596 | 3.3413 | -1.1877 | 5 | 0.3666 | 0.0844 | 0.3179 | 0.4645 | -0.1313 | 0.9548 | -0.0375 | 0.0745 | 0.0971 | 0.0733 | -0.0099 | -0.0437 | -0.0135 | 0.1212 | 0.0282 | 0.0926 | 0.0002 | -0.0035 | 0.0566 | 0.0038 | 0.0843 | 23.6256 | -2.1415 | 5.5719 | 6 | 0.3464 | 0.2681 | 0.0184 | 0.1846 | -0.0971 | 0.9488 | -0.0187 | 0.059 | 0.1078 | -0.0091 | -0.0045 | 0.1859 | 0.1846 | -0.2161 | -0.038 | 0.0812 | -0.0068 | 0.0166 | 0.1513 | -0.0147 | 0.1803 | 3.9701 | -3.9031 | 5.9174 | 7 | 0.4781 | 0.0869 | 0.2134 | 0.0173 | -0.0166 | 0.4024 | -0.0162 | -0.1306 | -0.1163 | -0.0311 | 0.0086 | 0.0407 | 0.2057 | 0.0434 | -0.0215 | 0.1354 | -0.0068 | 0.001 | 0.1174 | -0.0138 | 0.1025 | 20.3776 | -11.1718 | 12.9887 | 8 | 0.373 | 0.0774 | 0.1855 | 0.1057 | -0.0882 | 0.551 | 0.266 | -0.0083 | -0.0199 | -0.2019 | -0.1609 | -0.0559 | 0.5488 | 0.2282 | -0.0129 | 0.1672 | -0.1033 | -0.0571 | 0.0061 | -0.0343 | 0.0679 | 11.4663 | -14.0744 | 2.2813 | 9 | 0.3773 | 0.0142 | 0.4308 | 0.5991 | 0.2792 | 0.5331 | 0.0687 | 0.3966 | -0.196 | 0.751 | -0.1913 | -0.0372 | 0.1994 | 0.316 | 0.0021 | 0.1278 | 0.0494 | 0.0013 | -0.1928 | -0.0744 | 0.117 | 16.9587 | -15.9405 | 10.2886 | 10 | 0.7465 | -0.9753 | 0.6039 | 2.5333 | -1.5347 | 1.2318 | -0.1907 | 0.2008 | 0.1756 | 0.5459 | 0.1213 | -0.8317 | -0.1834 | -0.1405 | 0.1037 | 0.1523 | -0.0196 | -0.0929 | 0.0292 | -0.04 | 0.2005 | 19.8169 | -21.4811 | -27.194 | 11 | 0.4231 | -0.2556 | 0.0592 | 0.6267 | 0.5484 | 0.5176 | -0.0133 | -0.0784 | 0.0424 | 0.0716 | 0.0467 | -0.0991 | 0.0726 | 0.009 | -0.0254 | 0.0901 | -0.002 | -0.0194 | 0.0877 | -0.0061 | 0.0868 | 9.0063 | -15.4874 | -16.5763 | 12 | 0.312 | -0.0652 | 0.1148 | 0.4279 | 0.2616 | 0.7837 | -0.0634 | 0.0386 | 0.0183 | -0.0396 | -0.0355 | -0.0826 | -0.037 | 0.007 | 0.0467 | 0.0626 | 0.0087 | -0.0003 | 0.0549 | -0.0106 | 0.0642 | 7.1061 | -22.761 | -32.1372 | 13 | 0.8464 | -0.1144 | 0.0134 | 0.0033 | -0.0526 | 1.0181 | 0.1176 | 0.1207 | -0.211 | -0.1366 | -0.078 | 0.0976 | 0.3942 | 0.0756 | -0.0224 | 0.1787 | -0.0087 | -0.0314 | 0.0555 | -0.0215 | 0.1147 | -2.1451 | -26.6205 | -24.1196 | 14 | 0.7429 | -0.1817 | -0.0159 | 0.2766 | -0.4766 | 1.5228 | -0.0161 | -0.0563 | 0.011 | 0.2042 | -0.0185 | -0.0718 | -0.2978 | -0.1096 | 0.0118 | 0.0727 | -0.0024 | 0.0087 | 0.0418 | -0.0012 | 0.0446 | -0.8337 | -8.4856 | -17.5906 | 15 | 0.5925 | -0.382 | -0.2265 | 0.5365 | -0.4464 | 1.7674 | -0.1517 | 0.065 | -0.0723 | 0.0831 | 0.0824 | 0.1671 | -0.2108 | -0.4714 | 0.0012 | 0.0713 | 0.018 | 0.0184 | 0.1269 | -0.0055 | 0.0902 | -9.1007 | -8.2405 | -20.4206 |
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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 (resseq 4:22)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 23:62)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 63:91)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 92:121)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 122:138)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 139:150)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 151:164)8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resseq 165:188)9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resseq 189:202)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 3:22)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 23:62)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 63:103)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 104:121)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 122:172)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 173:200) | | | | | | | | | | | | | | |
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