ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0267精密化 | XDS | | データ削減 | SCALA | | データスケーリング | MOLREP | | 位相決定 | Coot | | 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: AlphaFold2 model 解像度: 1.47→33.547 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.375 / SU ML: 0.062 / 交差検証法: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.084 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2484 | 2686 | 5.013 % |
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Rwork | 0.2244 | 50895 | - |
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all | 0.226 | - | - |
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obs | - | 53581 | 96.454 % |
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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 / 溶媒モデル: BABINET MODEL PLUS MASK |
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原子変位パラメータ | Biso mean: 21.258 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.6 Å2 | 0 Å2 | 0.134 Å2 |
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2- | - | -1.848 Å2 | -0 Å2 |
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3- | - | - | 2.386 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.47→33.547 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2317 | 0 | 24 | 152 | 2493 |
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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_d0.012 | 0.013 | 2457 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.016 | 2203 | X-RAY DIFFRACTION | r_angle_refined_deg1.729 | 1.651 | 3344 | X-RAY DIFFRACTION | r_angle_other_deg1.457 | 1.58 | 5085 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg8.001 | 5 | 289 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.856 | 23.624 | 149 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.794 | 15 | 387 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg12.439 | 15 | 10 | X-RAY DIFFRACTION | r_chiral_restr0.081 | 0.2 | 311 | X-RAY DIFFRACTION | r_gen_planes_refined0.012 | 0.02 | 2812 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 616 | X-RAY DIFFRACTION | r_nbd_refined0.203 | 0.2 | 396 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.188 | 0.2 | 2106 | X-RAY DIFFRACTION | r_nbtor_refined0.185 | 0.2 | 1137 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.085 | 0.2 | 1176 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.141 | 0.2 | 135 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.116 | 0.2 | 13 | X-RAY DIFFRACTION | r_nbd_other0.141 | 0.2 | 61 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.117 | 0.2 | 11 | X-RAY DIFFRACTION | r_mcbond_it0.82 | 1.042 | 1126 | X-RAY DIFFRACTION | r_mcbond_other0.814 | 1.04 | 1125 | X-RAY DIFFRACTION | r_mcangle_it1.337 | 1.558 | 1407 | X-RAY DIFFRACTION | r_mcangle_other1.337 | 1.56 | 1408 | X-RAY DIFFRACTION | r_scbond_it1.151 | 1.242 | 1331 | X-RAY DIFFRACTION | r_scbond_other1.151 | 1.244 | 1332 | X-RAY DIFFRACTION | r_scangle_it1.803 | 1.796 | 1931 | X-RAY DIFFRACTION | r_scangle_other1.802 | 1.798 | 1932 | X-RAY DIFFRACTION | r_lrange_it4.226 | 12.647 | 2680 | X-RAY DIFFRACTION | r_lrange_other4.203 | 12.44 | 2660 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.47-1.508 | 0.359 | 145 | 0.3 | 2963 | X-RAY DIFFRACTION | 75.7864 | 1.508-1.549 | 0.277 | 158 | 0.28 | 3394 | X-RAY DIFFRACTION | 89.4035 | 1.549-1.594 | 0.273 | 201 | 0.271 | 3423 | X-RAY DIFFRACTION | 94.081 | 1.594-1.643 | 0.279 | 215 | 0.258 | 3495 | X-RAY DIFFRACTION | 96.8163 | 1.643-1.697 | 0.261 | 194 | 0.242 | 3373 | X-RAY DIFFRACTION | 98.5904 | 1.697-1.757 | 0.293 | 171 | 0.246 | 3344 | X-RAY DIFFRACTION | 99.3218 | 1.757-1.823 | 0.267 | 165 | 0.257 | 3230 | X-RAY DIFFRACTION | 99.211 | 1.823-1.898 | 0.287 | 172 | 0.248 | 3050 | X-RAY DIFFRACTION | 99.047 | 1.898-1.982 | 0.225 | 152 | 0.229 | 2986 | X-RAY DIFFRACTION | 99.5558 | 1.982-2.079 | 0.249 | 161 | 0.229 | 2856 | X-RAY DIFFRACTION | 99.5381 | 2.079-2.191 | 0.251 | 124 | 0.224 | 2765 | X-RAY DIFFRACTION | 99.7583 | 2.191-2.324 | 0.259 | 131 | 0.216 | 2561 | X-RAY DIFFRACTION | 99.7406 | 2.324-2.484 | 0.265 | 131 | 0.227 | 2416 | X-RAY DIFFRACTION | 99.7259 | 2.484-2.683 | 0.242 | 145 | 0.221 | 2220 | X-RAY DIFFRACTION | 99.6629 | 2.683-2.938 | 0.247 | 110 | 0.218 | 2083 | X-RAY DIFFRACTION | 99.8179 | 2.938-3.285 | 0.248 | 93 | 0.22 | 1913 | X-RAY DIFFRACTION | 100 | 3.285-3.792 | 0.214 | 66 | 0.211 | 1670 | X-RAY DIFFRACTION | 99.9424 | 3.792-4.641 | 0.195 | 74 | 0.183 | 1423 | X-RAY DIFFRACTION | 99.8 | 4.641-6.552 | 0.268 | 52 | 0.221 | 1112 | X-RAY DIFFRACTION | 99.5723 | 6.552-33.547 | 0.277 | 26 | 0.253 | 618 | X-RAY DIFFRACTION | 99.5363 |
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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 | 1.6414 | 1.0281 | 0.3366 | 5.929 | 1.0295 | 2.134 | -0.0295 | -0.0175 | 0.0876 | -0.0728 | -0.0586 | 0.3582 | -0.0642 | -0.1483 | 0.0881 | 0.054 | 0.0046 | 0.006 | 0.1472 | -0.0014 | 0.09 | 5.1003 | 1.3202 | 4.7377 | 2 | 0.8737 | 0.1999 | 0.3612 | 2.1063 | 0.1288 | 0.3911 | 0.0327 | -0.1188 | -0.0574 | 0.3235 | -0.0484 | 0.1721 | 0.0865 | -0.091 | 0.0157 | 0.1393 | -0.0086 | 0.0275 | 0.1714 | -0.0003 | 0.0264 | 11.1505 | -0.4969 | 15.593 | 3 | 0.5104 | 0.2535 | 0.259 | 2.3253 | 0.9075 | 1.1604 | 0.0156 | 0.0071 | 0.0099 | -0.0506 | -0.0805 | 0.1606 | 0.0143 | -0.0915 | 0.0649 | 0.0977 | 0.0011 | -0.0049 | 0.1449 | -0.0052 | 0.0389 | 12.0297 | -1.6127 | 1.9207 | 4 | 0.0664 | 0.2873 | 0.1266 | 2.1177 | 0.8024 | 1.3404 | 0.0381 | -0.0065 | -0.0353 | -0.0558 | 0.0294 | -0.1825 | 0.0084 | 0.0533 | -0.0675 | 0.1008 | 0.0005 | -0.0114 | 0.1418 | -0.0065 | 0.0269 | 20.7617 | -2.8272 | 4.3263 | 5 | 0.5216 | -0.0346 | 0.2756 | 1.3848 | 0.545 | 0.3772 | 0.0279 | 0.0792 | 0.0212 | -0.0685 | -0.0039 | -0.0891 | -0.0096 | 0.0589 | -0.024 | 0.1352 | -0.0072 | 0.0054 | 0.1538 | 0.0004 | 0.0108 | 19.3219 | -0.0071 | -1.4145 | 6 | 1.149 | 0.0544 | 0.3831 | 1.6189 | -0.0281 | 0.7864 | 0.0313 | -0.0184 | -0.0727 | 0.2237 | -0.0091 | 0.0065 | -0.0278 | 0.0228 | -0.0222 | 0.1173 | -0.0022 | -0.0104 | 0.1551 | 0.0054 | 0.0059 | 19.3795 | 3.6006 | 13.7109 | 7 | 1.2468 | -1.9593 | 2.6394 | 5.9858 | 1.0271 | 18.4779 | 0.0842 | 0.1095 | -0.0486 | -0.4002 | -0.1734 | 0.5661 | 0.1802 | -0.274 | 0.0892 | 0.1676 | -0.0601 | -0.1078 | 0.1682 | 0.067 | 0.224 | 7.4267 | 0.4226 | -5.8308 | 8 | 1.6138 | 0.4764 | 0.3975 | 7.5928 | 0.9378 | 1.7608 | 0.0023 | 0.0459 | -0.0359 | 0.0064 | 0.0271 | 0.2315 | 0.0527 | -0.0896 | -0.0295 | 0.0611 | -0.0122 | -0.0189 | 0.1756 | 0.0023 | 0.0757 | 17.7804 | -32.4003 | 34.9558 | 9 | 0.4837 | -0.5962 | 0.3578 | 1.3712 | -0.2236 | 0.5464 | 0.0736 | 0.0598 | 0.0603 | -0.23 | -0.1289 | 0.0625 | -0.0027 | -0.0249 | 0.0553 | 0.1495 | 0.0031 | -0.0287 | 0.1896 | 0.0091 | 0.0439 | 23.9897 | -29.985 | 24.2607 | 10 | 0.5859 | -0.5487 | 0.0958 | 3.379 | 0.8547 | 1.5196 | 0.0128 | -0.002 | 0.0065 | 0.1247 | -0.063 | 0.0486 | 0.0068 | -0.1045 | 0.0502 | 0.1116 | -0.0126 | -0.0194 | 0.1634 | 0.0074 | 0.0071 | 24.497 | -29.6037 | 38.1023 | 11 | 0.0695 | -0.1475 | 0.2331 | 2.0438 | 0.3286 | 1.2458 | 0.0136 | 0.037 | 0.0311 | 0.0981 | -0.0617 | -0.2162 | 0.037 | 0.0689 | 0.0482 | 0.1083 | -0.0046 | -0.0212 | 0.159 | 0.0101 | 0.0309 | 33.9668 | -28.4791 | 35.0722 | 12 | 1.9329 | 0.3775 | -0.3921 | 1.6989 | 0.681 | 0.4341 | 0.1263 | -0.0858 | -0.0879 | 0.2168 | -0.0704 | -0.201 | 0.0519 | -0.005 | -0.0559 | 0.209 | 0.0021 | -0.0758 | 0.1597 | 0.0218 | 0.0394 | 31.8995 | -31.3835 | 41.7556 | 13 | 0.757 | -0.8709 | -0.2902 | 1.7796 | 0.0469 | 0.5129 | 0.0473 | 0.0396 | 0.1303 | -0.0385 | -0.013 | -0.0351 | 0.1065 | -0.0623 | -0.0342 | 0.1335 | -0.0117 | 0.0117 | 0.1742 | 0.0011 | 0.0563 | 28.1626 | -32.6307 | 32.433 |
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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 | ALLA409 - 421 | 2 | X-RAY DIFFRACTION | 2 | ALLA422 - 454 | 3 | X-RAY DIFFRACTION | 3 | ALLA455 - 476 | 4 | X-RAY DIFFRACTION | 4 | ALLA477 - 502 | 5 | X-RAY DIFFRACTION | 5 | ALLA503 - 526 | 6 | X-RAY DIFFRACTION | 6 | ALLA527 - 541 | 7 | X-RAY DIFFRACTION | 7 | ALLA542 - 547 | 8 | X-RAY DIFFRACTION | 8 | ALLB409 - 421 | 9 | X-RAY DIFFRACTION | 9 | ALLB422 - 456 | 10 | X-RAY DIFFRACTION | 10 | ALLB457 - 476 | 11 | X-RAY DIFFRACTION | 11 | ALLB477 - 503 | 12 | X-RAY DIFFRACTION | 12 | ALLB504 - 524 | 13 | X-RAY DIFFRACTION | 13 | ALLB525 - 548 | | | | | | | | | | | | | | | | | | | | | | | | | | |
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