ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0258精密化 | HKL-2000 | | データ削減 | HKL-2000 | | 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: 3IXF 解像度: 1.67→33.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.579 / SU ML: 0.052 / 交差検証法: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.022 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1884 | 1546 | 4.956 % |
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Rwork | 0.1683 | - | - |
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all | 0.169 | - | - |
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obs | - | 31197 | 94.531 % |
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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: 1.2 Å |
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原子変位パラメータ | Biso mean: 17.85 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 6.225 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -2.455 Å2 | 0 Å2 |
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3- | - | - | -3.77 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.67→33.77 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2155 | 0 | 120 | 157 | 2432 |
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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_d0.009 | 0.013 | 2842 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.018 | 2549 | X-RAY DIFFRACTION | r_angle_refined_deg1.73 | 1.648 | 3912 | X-RAY DIFFRACTION | r_angle_other_deg1.457 | 1.583 | 5990 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.478 | 5 | 383 | X-RAY DIFFRACTION | r_dihedral_angle_other_1_deg12.796 | 10 | 2 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.578 | 22.675 | 157 | X-RAY DIFFRACTION | r_dihedral_angle_other_2_deg15.509 | 10 | 14 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg18.391 | 15 | 529 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg21.195 | 15 | 20 | X-RAY DIFFRACTION | r_chiral_restr0.091 | 0.2 | 341 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 3432 | X-RAY DIFFRACTION | r_gen_planes_other0.003 | 0.02 | 636 | X-RAY DIFFRACTION | r_nbd_refined0.246 | 0.2 | 724 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.179 | 0.2 | 2269 | X-RAY DIFFRACTION | r_nbtor_refined0.169 | 0.2 | 1325 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.08 | 0.2 | 999 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.19 | 0.2 | 129 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.048 | 0.2 | 2 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.229 | 0.2 | 21 | X-RAY DIFFRACTION | r_nbd_other0.22 | 0.2 | 66 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.143 | 0.2 | 21 | X-RAY DIFFRACTION | r_mcbond_it0.544 | 1.175 | 1340 | X-RAY DIFFRACTION | r_mcbond_other0.542 | 1.174 | 1339 | X-RAY DIFFRACTION | r_mcangle_it0.866 | 1.761 | 1739 | X-RAY DIFFRACTION | r_mcangle_other0.866 | 1.762 | 1740 | X-RAY DIFFRACTION | r_scbond_it0.816 | 1.332 | 1502 | X-RAY DIFFRACTION | r_scbond_other0.804 | 1.327 | 1495 | X-RAY DIFFRACTION | r_scangle_it1.253 | 1.977 | 2151 | X-RAY DIFFRACTION | r_scangle_other1.234 | 1.969 | 2140 | X-RAY DIFFRACTION | r_lrange_it3.077 | 14.446 | 3463 | X-RAY DIFFRACTION | r_lrange_other3.036 | 14.363 | 3449 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.67-1.71 | 0.29 | 103 | 0.3 | 2039 | X-RAY DIFFRACTION | 88.6223 | 1.71-1.757 | 0.307 | 126 | 0.287 | 2098 | X-RAY DIFFRACTION | 95.6148 | 1.757-1.808 | 0.256 | 107 | 0.223 | 2074 | X-RAY DIFFRACTION | 95.3234 | 1.808-1.864 | 0.222 | 96 | 0.192 | 2031 | X-RAY DIFFRACTION | 96.594 | 1.864-1.925 | 0.208 | 123 | 0.196 | 1958 | X-RAY DIFFRACTION | 96.2535 | 1.925-1.992 | 0.192 | 114 | 0.169 | 1880 | X-RAY DIFFRACTION | 96.282 | 1.992-2.067 | 0.204 | 101 | 0.156 | 1826 | X-RAY DIFFRACTION | 95.9661 | 2.067-2.152 | 0.171 | 79 | 0.142 | 1781 | X-RAY DIFFRACTION | 95.9752 | 2.152-2.247 | 0.213 | 78 | 0.149 | 1711 | X-RAY DIFFRACTION | 95.0584 | 2.247-2.356 | 0.144 | 99 | 0.15 | 1604 | X-RAY DIFFRACTION | 96.1061 | 2.356-2.484 | 0.195 | 95 | 0.145 | 1512 | X-RAY DIFFRACTION | 94.5851 | 2.484-2.634 | 0.172 | 83 | 0.139 | 1451 | X-RAY DIFFRACTION | 95.0434 | 2.634-2.815 | 0.154 | 73 | 0.146 | 1393 | X-RAY DIFFRACTION | 95.6295 | 2.815-3.04 | 0.15 | 54 | 0.146 | 1279 | X-RAY DIFFRACTION | 94.1384 | 3.04-3.328 | 0.18 | 43 | 0.165 | 1193 | X-RAY DIFFRACTION | 94.4954 | 3.328-3.719 | 0.16 | 40 | 0.164 | 1085 | X-RAY DIFFRACTION | 93.75 | 3.719-4.29 | 0.195 | 38 | 0.144 | 952 | X-RAY DIFFRACTION | 92.093 | 4.29-5.244 | 0.216 | 38 | 0.165 | 794 | X-RAY DIFFRACTION | 91.3282 | 5.244-7.371 | 0.142 | 45 | 0.206 | 624 | X-RAY DIFFRACTION | 90.5277 | 7.371-33.77 | 0.196 | 11 | 0.231 | 366 | X-RAY DIFFRACTION | 85.4875 |
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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 | 0.5661 | -0.3047 | 0.2504 | 0.1767 | -0.0935 | 0.5151 | -0.0249 | -0.0034 | -0.0162 | 0.0053 | 0.0073 | -0.0045 | -0.0019 | -0.0283 | 0.0176 | 0.0856 | -0.0023 | 0.0012 | 0.0522 | 0.0116 | 0.0669 | -0.2637 | -1.5635 | -23.9519 | 2 | 1.0716 | -1.3854 | -0.944 | 1.8637 | 1.5817 | 2.8463 | -0.1157 | -0.0092 | 0.1818 | 0.1367 | 0.0634 | -0.2223 | 0.0343 | 0.2385 | 0.0523 | 0.1079 | 0.008 | -0.0293 | 0.0353 | -0.0007 | 0.1327 | 16.0815 | -4.6879 | -15.3912 | 3 | 8.6631 | 4.0018 | -1.766 | 2.4867 | -1.8892 | 3.853 | 0.0227 | -0.2063 | 0.224 | 0.0324 | -0.1616 | 0.0455 | 0.0281 | 0.2282 | 0.1388 | 0.0801 | 0.0004 | -0.0348 | 0.0486 | -0.0292 | 0.0673 | 11.7934 | -0.9556 | -6.949 | 4 | 3.224 | -0.4606 | -0.0961 | 1.4338 | 0.3333 | 0.0776 | -0.0417 | -0.0438 | 0.0128 | 0.1194 | 0.0266 | 0.0571 | 0.0289 | 0.0064 | 0.0152 | 0.0832 | -0.0021 | 0.0002 | 0.0493 | 0.0036 | 0.0577 | 5.2881 | -10.5761 | -9.5724 | 5 | 0.0103 | -0.1431 | 0.1152 | 2.2448 | -2.202 | 2.7916 | -0.0021 | 0.0028 | 0.0024 | 0.0408 | -0.0335 | -0.0038 | -0.0356 | 0.0271 | 0.0356 | 0.0799 | -0.0021 | 0.0012 | 0.0512 | 0.004 | 0.0675 | -0.309 | 3.893 | -16.7513 | 6 | 1.4358 | -0.0069 | 0.6408 | 0.0275 | 0.2321 | 2.4204 | 0.0276 | -0.0374 | 0.0017 | -0.0039 | -0.0186 | -0.0098 | -0.0543 | -0.1383 | -0.0091 | 0.091 | -0.0106 | -0.0073 | 0.0404 | 0.0096 | 0.0676 | 4.9229 | 15.4277 | -26.6627 | 7 | 2.5395 | -1.9062 | -0.6726 | 1.5109 | -0.0104 | 3.4994 | -0.0788 | -0.076 | 0.0156 | 0.0841 | 0.0575 | -0.0156 | -0.0975 | 0.0577 | 0.0214 | 0.1143 | -0.0466 | -0.0183 | 0.0479 | 0.0033 | 0.0393 | 8.8834 | 13.6138 | -11.77 | 8 | 3.5565 | 1.4639 | 1.7895 | 2.1274 | 1.7767 | 1.6118 | -0.063 | -0.043 | 0.0153 | 0.0379 | 0.0799 | -0.0367 | 0.0137 | 0.0541 | -0.0169 | 0.0946 | 0.0049 | -0.0164 | 0.0402 | 0.0256 | 0.0768 | 15.4518 | 5.898 | -19.1426 | 9 | 1.6141 | 0.575 | 0.2091 | 2.2165 | 2.1928 | 2.266 | -0.0575 | 0.0462 | -0.0812 | 0.0351 | 0.0358 | -0.0019 | 0.0499 | 0.0535 | 0.0217 | 0.0961 | 0.0103 | 0.0176 | 0.0613 | 0.0141 | 0.0739 | 7.9344 | -3.3716 | -28.2048 | 10 | 2.3446 | 2.0185 | 1.2679 | 2.5646 | 1.2086 | 1.0253 | 0.0131 | 0.0917 | -0.034 | -0.0197 | -0.0473 | -0.0897 | 0.0315 | 0.0677 | 0.0342 | 0.0786 | 0.0076 | 0.0107 | 0.0401 | -0.0042 | 0.0704 | 6.5842 | 3.15 | -32.4037 | 11 | 1.5427 | 0.5661 | 1.3211 | 1.5399 | -0.6873 | 2.9797 | 0.0414 | 0.0536 | -0.0673 | -0.0036 | 0.0158 | -0.1779 | 0.0071 | 0.0794 | -0.0572 | 0.0906 | -0.0147 | -0.0165 | 0.011 | 0.01 | 0.102 | 14.6166 | 15.015 | -22.1041 | 12 | 0.3461 | 0.2104 | -0.1194 | 0.5556 | -0.2785 | 0.1488 | -0.0415 | -0.0276 | -0.0298 | 0.0098 | 0.0141 | -0.0628 | -0.0116 | -0.0243 | 0.0274 | 0.0895 | 0.0022 | -0.0002 | 0.0542 | 0.0062 | 0.0677 | -14.9932 | 7.4777 | -15.7243 | 13 | 2.5344 | 1.4443 | -2.3924 | 2.4895 | 0.0679 | 3.5663 | 0.014 | 0.0331 | 0.0261 | -0.1263 | -0.1281 | 0.2905 | -0.1813 | -0.2075 | 0.1141 | 0.1144 | -0.0068 | 0.0147 | 0.0827 | 0.0502 | 0.1544 | -31.2415 | 2.0682 | -11.3296 | 14 | 1.1544 | -0.5826 | 2.3806 | 3.5583 | -0.8116 | 4.9569 | 0.0465 | -0.067 | -0.3042 | 0.0758 | 0.5847 | 0.1561 | 0.1322 | -0.0799 | -0.6312 | 0.1385 | -0.0649 | -0.0046 | 0.1459 | 0.0128 | 0.0808 | -27.5477 | -8.3706 | -13.0304 | 15 | 1.5983 | 0.1332 | -2.2073 | 0.6828 | -0.7427 | 3.5154 | -0.0327 | -0.1356 | -0.0874 | -0.042 | -0.0108 | 0.0861 | 0.0784 | 0.177 | 0.0435 | 0.0807 | -0.0014 | -0.0051 | 0.0537 | 0.0104 | 0.0571 | -18.1635 | -6.9762 | -6.0611 | 16 | 1.1278 | -0.6212 | -0.0928 | 3.2329 | -0.4663 | 1.3633 | -0.0731 | 0.0729 | -0.1229 | -0.0564 | 0.0272 | 0.0966 | 0.0743 | 0.0517 | 0.0459 | 0.0815 | 0.0028 | -0.0012 | 0.0467 | 0.0117 | 0.0613 | -15.3084 | -3.6969 | -17.6587 | 17 | 0.8 | -0.5813 | 0.4418 | 1.7058 | -0.0779 | 0.2906 | 0.0178 | 0.0303 | 0.0168 | -0.0031 | -0.0211 | -0.0326 | 0.0055 | 0.0164 | 0.0033 | 0.0877 | 0.0019 | -0.0009 | 0.0553 | 0.0117 | 0.0571 | -17.5567 | 10.2264 | -29.0061 | 18 | 0.2435 | 0.3262 | 0.7354 | 2.1537 | 1.3989 | 2.3217 | 0.0941 | -0.0227 | -0.0713 | 0.0474 | 0.1413 | -0.2198 | 0.233 | -0.0316 | -0.2354 | 0.1087 | -0.003 | -0.0601 | 0.0283 | -0.0061 | 0.0916 | -23.2264 | 1.3746 | -32.6318 | 19 | 4.3892 | -3.2366 | -3.8292 | 3.4653 | 1.4427 | 5.1086 | -0.1938 | -0.0334 | -0.2908 | 0.1329 | -0.0199 | 0.2425 | 0.1659 | 0.0793 | 0.2137 | 0.1233 | -0.0283 | -0.0249 | 0.0099 | 0.0053 | 0.0934 | -28.1875 | -4.0256 | -26.7463 | 20 | 3.0131 | 2.5225 | 1.5674 | 2.1354 | 1.4481 | 2.2392 | 0.0495 | -0.0279 | 0.1096 | 0.0113 | 0.0005 | 0.079 | 0.0229 | -0.0586 | -0.05 | 0.1109 | -0.0164 | 0.003 | 0.0675 | 0.0025 | 0.0383 | -25.2197 | 9.916 | -15.4194 | 21 | 2.6515 | 1.3003 | 2.2124 | 0.7546 | 0.8071 | 2.5096 | 0.0093 | -0.0674 | 0.0902 | 0.0095 | -0.0162 | 0.0705 | 0.0029 | -0.0854 | 0.0069 | 0.0815 | 0.0039 | 0.0061 | 0.0511 | -0.0117 | 0.0602 | -22.2427 | 15.9036 | -20.2172 | 22 | 1.0262 | 0.3794 | 1.801 | 0.4284 | 1.1222 | 3.8952 | 0.1012 | -0.0683 | 0.0561 | -0.0227 | -0.0957 | -0.0367 | 0.1136 | -0.2229 | -0.0055 | 0.1124 | -0.0185 | -0.0099 | 0.0659 | 0.0083 | 0.04 | -30.5444 | 5.5279 | -31.4054 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA1 - 26 | 2 | X-RAY DIFFRACTION | 2 | ALLA27 - 33 | 3 | X-RAY DIFFRACTION | 3 | ALLA34 - 37 | 4 | X-RAY DIFFRACTION | 4 | ALLA38 - 48 | 5 | X-RAY DIFFRACTION | 5 | ALLA49 - 69 | 6 | X-RAY DIFFRACTION | 6 | ALLA70 - 83 | 7 | X-RAY DIFFRACTION | 7 | ALLA84 - 90 | 8 | X-RAY DIFFRACTION | 8 | ALLA91 - 99 | 9 | X-RAY DIFFRACTION | 9 | ALLA100 - 111 | 10 | X-RAY DIFFRACTION | 10 | ALLA112 - 128 | 11 | X-RAY DIFFRACTION | 11 | ALLA129 - 137 | 12 | X-RAY DIFFRACTION | 12 | ALLB1 - 26 | 13 | X-RAY DIFFRACTION | 13 | ALLB27 - 31 | 14 | X-RAY DIFFRACTION | 14 | ALLB32 - 39 | 15 | X-RAY DIFFRACTION | 15 | ALLB40 - 50 | 16 | X-RAY DIFFRACTION | 16 | ALLB51 - 60 | 17 | X-RAY DIFFRACTION | 17 | ALLB61 - 77 | 18 | X-RAY DIFFRACTION | 18 | ALLB78 - 86 | 19 | X-RAY DIFFRACTION | 19 | ALLB87 - 94 | 20 | X-RAY DIFFRACTION | 20 | ALLB95 - 111 | 21 | X-RAY DIFFRACTION | 21 | ALLB112 - 128 | 22 | X-RAY DIFFRACTION | 22 | ALLB129 - 137 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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