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: 1.15→32.545 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.451 / SU ML: 0.032 / 交差検証法: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.039 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2087 | 5719 | 5.035 % |
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Rwork | 0.1933 | 107860 | - |
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all | 0.194 | - | - |
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obs | - | 113579 | 98.625 % |
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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: 18.769 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.534 Å2 | 0 Å2 | -0.401 Å2 |
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2- | - | 0.215 Å2 | -0 Å2 |
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3- | - | - | -0.653 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.15→32.545 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2494 | 0 | 46 | 214 | 2754 |
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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_d0.011 | 0.013 | 2653 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.015 | 2377 | X-RAY DIFFRACTION | r_angle_refined_deg1.677 | 1.665 | 3606 | X-RAY DIFFRACTION | r_angle_other_deg1.423 | 1.594 | 5483 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.733 | 5 | 307 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.022 | 23.101 | 158 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.612 | 15 | 413 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.822 | 15 | 12 | X-RAY DIFFRACTION | r_chiral_restr0.077 | 0.2 | 340 | X-RAY DIFFRACTION | r_gen_planes_refined0.009 | 0.02 | 3010 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 660 | X-RAY DIFFRACTION | r_nbd_refined0.2 | 0.2 | 394 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.183 | 0.2 | 2195 | X-RAY DIFFRACTION | r_nbtor_refined0.18 | 0.2 | 1229 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.084 | 0.2 | 1300 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.115 | 0.2 | 162 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.239 | 0.2 | 39 | X-RAY DIFFRACTION | r_nbd_other0.209 | 0.2 | 142 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.143 | 0.2 | 10 | X-RAY DIFFRACTION | r_mcbond_it0.811 | 1.097 | 1211 | X-RAY DIFFRACTION | r_mcbond_other0.81 | 1.096 | 1210 | X-RAY DIFFRACTION | r_mcangle_it1.317 | 1.645 | 1511 | X-RAY DIFFRACTION | r_mcangle_other1.317 | 1.646 | 1512 | X-RAY DIFFRACTION | r_scbond_it1.264 | 1.324 | 1442 | X-RAY DIFFRACTION | r_scbond_other1.263 | 1.326 | 1443 | X-RAY DIFFRACTION | r_scangle_it1.998 | 1.912 | 2090 | X-RAY DIFFRACTION | r_scangle_other1.998 | 1.913 | 2091 | X-RAY DIFFRACTION | r_lrange_it4.199 | 13.677 | 2854 | X-RAY DIFFRACTION | r_lrange_other4.096 | 13.25 | 2813 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.15-1.18 | 0.288 | 420 | 0.285 | 7566 | X-RAY DIFFRACTION | 93.7214 | 1.18-1.212 | 0.289 | 411 | 0.273 | 7560 | X-RAY DIFFRACTION | 96.2449 | 1.212-1.247 | 0.27 | 377 | 0.265 | 7478 | X-RAY DIFFRACTION | 97.9426 | 1.247-1.286 | 0.251 | 368 | 0.251 | 7294 | X-RAY DIFFRACTION | 98.0924 | 1.286-1.328 | 0.267 | 350 | 0.239 | 7101 | X-RAY DIFFRACTION | 98.5973 | 1.328-1.374 | 0.243 | 363 | 0.223 | 6921 | X-RAY DIFFRACTION | 98.7259 | 1.374-1.426 | 0.25 | 307 | 0.212 | 6683 | X-RAY DIFFRACTION | 98.8685 | 1.426-1.485 | 0.228 | 337 | 0.199 | 6430 | X-RAY DIFFRACTION | 99.3978 | 1.485-1.551 | 0.223 | 337 | 0.192 | 6162 | X-RAY DIFFRACTION | 99.4339 | 1.551-1.626 | 0.199 | 303 | 0.189 | 5909 | X-RAY DIFFRACTION | 99.5513 | 1.626-1.714 | 0.187 | 297 | 0.18 | 5665 | X-RAY DIFFRACTION | 99.8158 | 1.714-1.818 | 0.204 | 313 | 0.188 | 5295 | X-RAY DIFFRACTION | 99.8042 | 1.818-1.943 | 0.193 | 269 | 0.187 | 5022 | X-RAY DIFFRACTION | 99.9811 | 1.943-2.099 | 0.208 | 266 | 0.179 | 4628 | X-RAY DIFFRACTION | 100 | 2.099-2.299 | 0.196 | 252 | 0.174 | 4310 | X-RAY DIFFRACTION | 100 | 2.299-2.57 | 0.209 | 204 | 0.186 | 3908 | X-RAY DIFFRACTION | 100 | 2.57-2.967 | 0.218 | 183 | 0.196 | 3463 | X-RAY DIFFRACTION | 99.8904 | 2.967-3.633 | 0.195 | 168 | 0.187 | 2925 | X-RAY DIFFRACTION | 99.8064 | 3.633-5.133 | 0.165 | 114 | 0.171 | 2264 | X-RAY DIFFRACTION | 100 | 5.133-32.545 | 0.245 | 80 | 0.211 | 1277 | X-RAY DIFFRACTION | 99.7061 |
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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 | 0.127 | 0.2087 | -0.2445 | 0.906 | 0.0476 | 1.0387 | 0.0426 | -0.0093 | 0.0019 | 0.1952 | -0.0371 | 0.1606 | 0.0165 | -0.0525 | -0.0056 | 0.0449 | 0.0033 | 0.0315 | 0.0629 | 0.015 | 0.1232 | 10.3334 | 1.6567 | 15.3494 | 2 | 0.2835 | -0.0443 | 0.1807 | 1.0141 | 0.2547 | 1.1595 | 0.0056 | 0.0027 | -0.0307 | -0.0605 | 0.0085 | 0.0058 | -0.021 | 0.0571 | -0.0141 | 0.0355 | -0.0014 | -0.001 | 0.0511 | -0.0075 | 0.066 | 17.573 | 0.3307 | 2.7247 | 3 | 0.04 | 0.1456 | -0.1012 | 1.2296 | 0.1143 | 1.8081 | -0.0003 | 0.0464 | 0.0432 | -0.0935 | -0.0242 | 0.2002 | 0.0718 | -0.212 | 0.0245 | 0.0196 | 0.0176 | -0.0017 | 0.1414 | 0.0209 | 0.0747 | 18.4873 | -32.859 | 27.5929 | 4 | 0.2044 | -0.0327 | 0.0184 | 1.3821 | 0.1361 | 1.2091 | 0.0444 | 0.0699 | 0.0493 | 0.1653 | -0.0815 | -0.0389 | 0.0517 | 0.1289 | 0.0371 | 0.0376 | -0.001 | -0.0013 | 0.0793 | 0.01 | 0.067 | 29.4354 | -29.7547 | 35.9223 |
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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 | ALLA392 - 460 | 2 | X-RAY DIFFRACTION | 2 | ALLA461 - 547 | 3 | X-RAY DIFFRACTION | 3 | ALLB401 - 448 | 4 | X-RAY DIFFRACTION | 4 | ALLB449 - 548 | | | | | | | | |
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