ソフトウェア | 名称 | バージョン | 分類 | NB |
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SAINT | | データスケーリング | | MOLREP | | 位相決定 | | REFMAC | refmac_5.2.0019精密化 | | PDB_EXTRACT | 1.7 | データ抽出 | | PROTEUM PLUS | 2 | データ削減 | | SADABS | | データスケーリング | | XPREP | | データ削減 | | Coot | | モデル構築 | | MolProbity | | モデル構築 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 2TRX 解像度: 2.4→44.82 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.186 / SU B: 18.311 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.282 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2575 | 1014 | 9.978 % | Random |
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Rwork | 0.2007 | - | - | - |
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all | 0.206 | 10198 | - | - |
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obs | 0.206 | 10162 | 99.471 % | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK BULK SOLVENT |
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原子変位パラメータ | Biso mean: 20.845 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.785 Å2 | -1.392 Å2 | 0 Å2 |
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2- | - | -2.785 Å2 | 0 Å2 |
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3- | - | - | 4.177 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.4→44.82 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1629 | 0 | 16 | 60 | 1705 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.029 | 0.022 | 1739 | X-RAY DIFFRACTION | r_angle_refined_deg1.597 | 1.992 | 2365 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.908 | 5 | 224 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.013 | 27.101 | 69 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.221 | 15 | 301 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg4.366 | 15 | 1 | X-RAY DIFFRACTION | r_chiral_restr0.094 | 0.2 | 274 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 1277 | X-RAY DIFFRACTION | r_nbd_refined0.22 | 0.2 | 688 | X-RAY DIFFRACTION | r_nbtor_refined0.304 | 0.2 | 1143 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.204 | 0.2 | 77 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.214 | 0.2 | 28 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.161 | 0.2 | 7 | X-RAY DIFFRACTION | r_mcbond_it1.27 | 2 | 1150 | X-RAY DIFFRACTION | r_mcangle_it1.93 | 3 | 1775 | X-RAY DIFFRACTION | r_scbond_it1.226 | 2 | 684 | X-RAY DIFFRACTION | r_scangle_it1.789 | 3 | 588 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Rfactor all | Num. reflection all | % reflection obs (%) |
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2.4-2.462 | 0.376 | 82 | 0.238 | 663 | 0.254 | 763 | 97.641 | 2.462-2.529 | 0.392 | 72 | 0.242 | 642 | 0.258 | 714 | 100 | 2.529-2.603 | 0.383 | 76 | 0.246 | 645 | 0.259 | 723 | 99.723 | 2.603-2.682 | 0.31 | 69 | 0.22 | 578 | 0.23 | 652 | 99.233 | 2.682-2.77 | 0.305 | 77 | 0.25 | 613 | 0.256 | 690 | 100 | 2.77-2.867 | 0.363 | 67 | 0.225 | 569 | 0.239 | 637 | 99.843 | 2.867-2.975 | 0.347 | 60 | 0.24 | 562 | 0.249 | 622 | 100 | 2.975-3.095 | 0.264 | 52 | 0.205 | 546 | 0.21 | 598 | 100 | 3.095-3.232 | 0.224 | 62 | 0.19 | 523 | 0.193 | 586 | 99.829 | 3.232-3.389 | 0.231 | 62 | 0.2 | 484 | 0.204 | 546 | 100 | 3.389-3.571 | 0.215 | 50 | 0.188 | 477 | 0.191 | 528 | 99.811 | 3.571-3.787 | 0.251 | 55 | 0.174 | 444 | 0.183 | 502 | 99.402 | 3.787-4.046 | 0.237 | 39 | 0.172 | 417 | 0.178 | 458 | 99.563 | 4.046-4.367 | 0.178 | 40 | 0.157 | 410 | 0.159 | 450 | 100 | 4.367-4.779 | 0.237 | 42 | 0.148 | 359 | 0.157 | 401 | 100 | 4.779-5.336 | 0.249 | 26 | 0.181 | 351 | 0.185 | 377 | 100 | 5.336-6.147 | 0.254 | 31 | 0.234 | 294 | 0.236 | 325 | 100 | 6.147-7.493 | 0.252 | 28 | 0.23 | 254 | 0.232 | 282 | 100 | 7.493-10.452 | 0.17 | 17 | 0.185 | 207 | 0.184 | 225 | 99.556 | 10.452-44.82 | 0.179 | 7 | 0.338 | 110 | 0.327 | 137 | 85.401 |
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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 | 17.9901 | -3.8842 | -2.9902 | 12.9911 | 0.4026 | 18.7709 | -0.9414 | -1.1508 | -1.7917 | 2.1483 | 0.1228 | -0.7274 | 0.4474 | 0.2017 | 0.8187 | 0.0585 | -0.0003 | -0.0666 | -0.1537 | 0.2782 | 0.2699 | 8.0323 | 18.8324 | 24.6024 | 2 | 4.4077 | -2.6362 | 0.0133 | 8.079 | -1.9035 | 0.5526 | 0.1914 | 0.4999 | -0.5814 | -0.7159 | -0.0949 | 0.5191 | 0.2196 | -0.423 | -0.0964 | -0.0916 | -0.0592 | -0.0785 | -0.0492 | -0.0551 | 0.0247 | 0.445 | 20.2019 | 13.175 | 3 | 11.2031 | -1.6697 | -0.8818 | 1.8705 | -0.1193 | 1.2037 | -0.0387 | 0.0215 | -0.7362 | -0.1076 | -0.0417 | -0.229 | 0.0671 | 0.0015 | 0.0803 | -0.1869 | 0.0071 | 0.0032 | -0.1745 | 0.0131 | -0.0237 | 5.8319 | 26.9396 | 18.2792 | 4 | 13.7896 | 1.0901 | -5.1648 | 2.8677 | -2.7664 | 11.2245 | 0.345 | -1.1009 | -0.4322 | 0.7519 | -0.3091 | -1.2819 | -0.6233 | 0.4533 | -0.0359 | -0.0997 | -0.0364 | -0.1353 | -0.1081 | 0.0751 | 0.1253 | 14.1672 | 29.6652 | 26.3249 | 5 | 7.9071 | -1.2036 | -5.3467 | 6.3903 | 4.6326 | 5.9648 | 0.3503 | -0.5613 | -0.8622 | 0.7588 | -0.0636 | -0.1907 | 0.0823 | 0.0539 | -0.2868 | -0.0644 | -0.0203 | -0.0876 | -0.093 | 0.1649 | 0.0689 | 4.2011 | 24.88 | 28.4759 | 6 | 11.6756 | -3.6506 | -1.1211 | 4.034 | 0.9868 | 0.2476 | 0.115 | 1.049 | -0.3375 | -0.242 | 0.0052 | 0.0296 | 0.0034 | -0.1392 | -0.1202 | -0.0855 | 0.009 | 0.0085 | 0.012 | 0.0525 | -0.134 | 6.8712 | 27.9574 | 9.2795 | 7 | 11.2444 | -0.1309 | 0.2293 | 3.9151 | 1.1576 | 0.3487 | 0.1779 | 0.5548 | 0.0523 | -0.1979 | -0.1476 | -0.2239 | -0.2472 | -0.1131 | -0.0303 | -0.119 | 0.0077 | -0.0521 | -0.1503 | 0.0348 | -0.0852 | 4.1665 | 33.4748 | 17.4334 | 8 | 5.895 | 2.6308 | 0.7736 | 6.1332 | -1.0164 | 6.4869 | -0.2317 | 0.2837 | -0.1 | -0.0338 | 0.0587 | 0.1 | -0.1661 | -0.2368 | 0.173 | -0.1869 | 0.014 | -0.0198 | -0.1787 | 0.0268 | -0.0925 | -3.0841 | 33.5004 | 19.8481 | 9 | 6.9441 | 1.434 | -2.2342 | 4.9404 | -1.5512 | 15.7968 | 0.0184 | -0.726 | 0.3467 | 0.4859 | -0.1344 | -0.7283 | -0.2602 | 0.2444 | 0.116 | -0.0428 | -0.0325 | -0.1562 | -0.1406 | 0.0126 | 0.0133 | 8.1293 | 37.4694 | 28.3723 | 10 | 26.4897 | -16.2059 | 3.1536 | 10.9563 | 1.8847 | 14.3378 | 0.1215 | -1.4617 | 0.1215 | 1.1174 | -0.0551 | -0.1335 | -0.6335 | -0.7458 | -0.0664 | 0.0239 | -0.0344 | -0.002 | -0.0863 | 0.0533 | -0.053 | -2.2448 | 35.223 | 30.1165 | 11 | 25.3382 | 23.2067 | -14.1174 | 21.2544 | -12.9297 | 7.8656 | -0.6995 | 0.5682 | 2.9473 | -2.988 | 0.3056 | -1.4038 | -1.2267 | -2.5372 | 0.3939 | 0.1085 | 0.2978 | -0.0781 | 0.2301 | 0.6522 | 0.3819 | -11.8267 | 51.4259 | 6.0737 | 12 | 13.8142 | 5.9901 | 0.0316 | 3.0293 | 1.7641 | 7.0948 | -0.3054 | -0.2826 | 2.2943 | 0.4029 | 0.3468 | -0.5844 | -0.7466 | -0.4413 | -0.0414 | 0.0966 | 0.0938 | -0.0922 | -0.0699 | 0.1294 | 0.5989 | -11.8451 | 57.3716 | 18.4046 | 13 | 1.4267 | -0.5705 | 0.7119 | 5.1909 | -2.3595 | 1.3957 | 0.0323 | -0.2711 | 0.1584 | 0.1082 | 0.3155 | 0.6763 | -0.2095 | -0.2124 | -0.3478 | 0.0394 | 0.0559 | -0.0635 | 0.0244 | 0.1721 | 0.1141 | -16.7568 | 50.5544 | 17.4025 | 14 | 7.1298 | 2.5114 | 5.0446 | 14.0229 | 10.256 | 9.0414 | 0.057 | 0.789 | 0.755 | -0.6276 | 0.0804 | -0.8467 | -0.5753 | -0.1173 | -0.1374 | -0.1138 | 0.0224 | 0.0184 | -0.0191 | 0.2191 | 0.0131 | -0.5096 | 42.3074 | 12.1088 | 15 | 42.2904 | -12.7339 | 4.5798 | 6.38 | -0.8558 | 0.6035 | 0.8563 | 1.6954 | 0.0386 | -1.4166 | -0.698 | 0.6204 | 0.151 | -0.2976 | -0.1584 | 0.0921 | 0.145 | -0.1933 | 0.3889 | 0.1746 | -0.0856 | -15.6186 | 41.7724 | 5.1223 | 16 | 12.0296 | -1.7691 | 6.2481 | 5.1675 | 2.6262 | 5.8062 | 0.069 | 0.3125 | 1.3772 | -0.4629 | -0.0793 | -0.1876 | -0.3997 | -0.3722 | 0.0103 | 0.0092 | 0.0384 | 0.0073 | -0.0294 | 0.2614 | 0.1735 | -9.7156 | 49.5926 | 13.8081 | 17 | 24.2103 | -0.1556 | -7.6325 | 9.8975 | 4.9942 | 4.8772 | -0.719 | -0.7576 | 1.0871 | 0.5337 | 0.341 | -0.0986 | -0.4358 | 0.362 | 0.3781 | 0.1162 | 0.1623 | -0.0952 | 0.0115 | 0.011 | -0.057 | -6.8573 | 48.7128 | 25.9445 | 18 | 12.841 | -2.7489 | -1.6633 | 7.834 | 1.4693 | 0.5608 | -0.5952 | -0.0699 | 0.5958 | 0.7184 | 0.3738 | 0.5886 | -0.3342 | -0.121 | 0.2214 | 0.0395 | 0.0577 | -0.0446 | -0.0914 | 0.1333 | -0.0084 | -15.9132 | 45.0809 | 21.463 | 19 | 9.1346 | -2.7625 | 2.6113 | 19.7312 | 2.2899 | 6.7637 | 0.2839 | 0.4617 | -0.5713 | -0.5142 | 0.1419 | 0.0462 | 0.1756 | 0.2693 | -0.4258 | -0.1081 | -0.0243 | -0.1327 | -0.1581 | 0.0779 | -0.0752 | -12.0142 | 35.6494 | 14.9314 | 20 | 20.4981 | 3.344 | -2.0116 | 6.3507 | -1.9755 | 9.218 | 0.58 | 0.0293 | -0.7544 | -0.6092 | -0.0886 | 1.0299 | -0.306 | -0.6157 | -0.4914 | -0.0467 | 0.0198 | -0.1603 | 0.0039 | 0.0958 | 0.0368 | -20.9117 | 36.157 | 14.3292 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Selection: ALL ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | AA1 - 7 | 1 - 7 | 2 | 2 | AA8 - 16 | 8 - 16 | 3 | 3 | AA17 - 33 | 17 - 33 | 4 | 4 | AA34 - 45 | 34 - 45 | 5 | 5 | AA46 - 58 | 46 - 58 | 6 | 6 | AA59 - 72 | 59 - 72 | 7 | 7 | AA73 - 82 | 73 - 82 | 8 | 8 | AA83 - 90 | 83 - 90 | 9 | 9 | AA91 - 102 | 91 - 102 | 10 | 10 | AA103 - 108 | 103 - 108 | 11 | 11 | BB1 - 6 | 1 - 6 | 12 | 12 | BB7 - 16 | 7 - 16 | 13 | 13 | BB17 - 27 | 17 - 27 | 14 | 14 | BB28 - 38 | 28 - 38 | 15 | 15 | BB39 - 50 | 39 - 50 | 16 | 16 | BB51 - 63 | 51 - 63 | 17 | 17 | BB64 - 73 | 64 - 73 | 18 | 18 | BB74 - 89 | 74 - 89 | 19 | 19 | BB90 - 97 | 90 - 97 | 20 | 20 | BB98 - 108 | 98 - 108 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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