ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データ収集 | SOLVE | | 位相決定 | REFMAC | 5.2.0019精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.08→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.549 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.176 / 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 | 0.26716 | 4081 | 5 % | RANDOM |
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Rwork | 0.22498 | - | - | - |
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obs | 0.22715 | 77311 | 99.3 % | - |
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all | - | 77854 | - | - |
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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 |
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原子変位パラメータ | Biso mean: 37.594 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.52 Å2 | 0 Å2 | -0.1 Å2 |
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2- | - | 1.6 Å2 | 0 Å2 |
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3- | - | - | -2.2 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.08→25 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6947 | 0 | 24 | 420 | 7391 |
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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 | 0.022 | 7150 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.246 | 1.992 | 9603 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.204 | 5 | 887 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg39.323 | 25.156 | 353 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.013 | 15.021 | 1431 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.058 | 15 | 52 | X-RAY DIFFRACTION | r_chiral_restr0.089 | 0.2 | 1091 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 5250 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.199 | 0.2 | 3597 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.295 | 0.2 | 5027 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.164 | 0.2 | 392 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.172 | 0.2 | 48 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.176 | 0.2 | 17 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.516 | 1.5 | 4539 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.801 | 2 | 7013 | X-RAY DIFFRACTION | r_scbond_it1.587 | 3 | 2941 | X-RAY DIFFRACTION | r_scangle_it2.44 | 4.5 | 2577 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.08→2.135 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.361 | 273 | - |
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Rwork | 0.313 | 5301 | - |
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obs | - | - | 92.64 % |
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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 | 18.6221 | -11.5989 | -2.0188 | 14.8562 | 12.9758 | 18.2124 | 0.4473 | 2.1718 | -0.1785 | -1.7984 | -0.6379 | 0.618 | -0.2403 | -0.3535 | 0.1906 | 0.4101 | -0.0943 | -0.016 | 0.5055 | 0.1574 | 0.3909 | -21.9935 | -5.4051 | -57.438 | 2 | 1.4733 | -0.1514 | -0.1597 | 6.6274 | -3.3994 | 2.892 | -0.0114 | -0.0163 | -0.1248 | 0.1396 | -0.0764 | -0.0443 | 0.0485 | 0.0434 | 0.0878 | -0.0922 | 0.0286 | 0.0557 | -0.071 | -0.0164 | -0.0631 | -19.6818 | -18.2293 | -32.5747 | 3 | 4.3577 | -0.0472 | -0.1705 | 1.6348 | 0.0638 | 2.0615 | 0.0893 | 0.3069 | 0.3366 | -0.0569 | -0.0656 | 0.0764 | -0.2642 | -0.0964 | -0.0237 | -0.0455 | 0.0384 | 0.0292 | -0.1074 | -0.0153 | -0.0124 | -33.166 | -2.0843 | -35.4735 | 4 | 5.3288 | -1.0617 | -0.5204 | 3.388 | -0.2314 | 2.7939 | 0.1559 | 0.3351 | -0.3346 | -0.1918 | -0.1311 | 0.1753 | 0.3678 | -0.2448 | -0.0248 | 0.0059 | 0.0138 | -0.0314 | -0.0059 | -0.0747 | 0.0946 | -45.6913 | -12.4374 | -38.5168 | 5 | 0.7305 | 1.7232 | -5.4303 | 4.0647 | -12.8094 | 40.3669 | -0.0469 | -1.2775 | -1.4293 | 1.9044 | -0.1703 | -0.3273 | -1.2531 | 1.9786 | 0.2172 | 0.4541 | -0.0776 | -0.0535 | 0.6263 | 0.1317 | 0.3602 | -7.7461 | -6.8541 | -26.2258 | 6 | 6.6206 | 3.8615 | -1.347 | 9.4909 | -2.7584 | 7.4889 | -0.133 | 0.445 | 0.5401 | -0.5842 | 0.0134 | -0.1416 | -0.3678 | 0.0106 | 0.1196 | -0.0168 | 0.029 | 0.0536 | 0.0052 | 0.0224 | 0.0088 | -10.4963 | -0.2573 | -47.6974 | 7 | 1.9654 | 1.4958 | -1.3313 | 4.5504 | -2.9142 | 3.1268 | -0.2017 | -0.0658 | -0.4706 | -0.1788 | -0.0599 | -0.182 | 0.5286 | 0.204 | 0.2616 | -0.0203 | 0.0413 | 0.0872 | -0.0594 | -0.017 | 0.0782 | -12.3806 | -26.6588 | -37.1612 | 8 | 2.1665 | -0.2402 | -0.1821 | 2.6264 | -1.2824 | 2.3578 | -0.0455 | 0.0871 | -0.0189 | -0.1476 | -0.1508 | -0.2254 | -0.0436 | 0.1314 | 0.1963 | -0.0534 | -0.0038 | 0.0283 | 0.0357 | 0.0196 | -0.0429 | 2.0991 | -8.5916 | -49.1477 | 9 | 3.551 | 1.0921 | 0.3071 | 10.8847 | 3.47 | 3.5298 | -0.052 | -0.4227 | 0.048 | 0.9231 | 0.0146 | -0.8428 | -0.081 | 0.0154 | 0.0374 | 0.1065 | 0.036 | -0.1651 | 0.2902 | 0.0867 | 0.1189 | 11.7791 | -4.9889 | -34.5797 | 10 | 12.0215 | -13.1724 | -5.4498 | 14.5631 | 7.699 | 25.507 | -1.2191 | -1.2299 | -1.7787 | 1.7579 | 1.0282 | 0.3593 | 1.6121 | 1.1621 | 0.1909 | 0.5467 | -0.0312 | -0.0603 | 0.5724 | 0.0999 | 0.3937 | 11.2303 | -12.6043 | -27.767 | 11 | 11.0571 | 2.2795 | -7.3956 | 8.179 | -10.7723 | 16.0398 | 0.3001 | 0.4626 | 0.529 | -0.1514 | 0.2078 | -0.8823 | -0.1254 | 1.5772 | -0.5079 | 0.5153 | -0.0332 | 0.1436 | 0.5553 | -0.0996 | 0.4158 | -26.0816 | 11.4024 | -9.4029 | 12 | 1.8311 | -2.7465 | -0.8361 | 6.5166 | 2.0326 | 2.3744 | 0.0416 | 0.0269 | 0.0115 | -0.0922 | -0.0655 | 0.0295 | -0.0269 | 0.0402 | 0.0239 | -0.0048 | 0.0062 | -0.007 | -0.0275 | 0.0296 | -0.1216 | -45.5651 | 22.541 | 6.7334 | 13 | 4.6581 | -1.236 | 0.773 | 3.1339 | 0.0424 | 3.1209 | 0.1482 | 0.2913 | -0.3125 | -0.1038 | -0.2207 | -0.3106 | 0.4289 | 0.441 | 0.0725 | 0.0897 | 0.048 | 0.019 | -0.043 | 0.0428 | -0.0204 | -33.3484 | 6.7728 | 13.8169 | 14 | 3.0116 | 0.1269 | 0.5598 | 4.5497 | 0.1664 | 4.8906 | 0.1225 | 0.0216 | 0.3005 | 0.1751 | -0.274 | -0.6967 | -0.1794 | 0.5967 | 0.1515 | 0.0468 | -0.0064 | -0.0335 | 0.0767 | 0.1036 | 0.1622 | -25.6728 | 17.4564 | 22.4309 | 15 | 3.6843 | 0.8911 | -0.0141 | 5.1258 | 3.2272 | 10.1199 | 0.1341 | 0.0024 | -0.3217 | -0.0574 | -0.2779 | 0.2782 | 0.3514 | -0.3255 | 0.1438 | 0.1474 | 0.0267 | -0.0055 | -0.0097 | 0.0306 | -0.0293 | -45.5942 | 6.7049 | -6.626 | 16 | 0.7086 | -0.0048 | -0.1921 | 1.4698 | 1.9109 | 3.6135 | -0.003 | 0.1021 | 0.067 | -0.257 | -0.089 | -0.039 | -0.495 | -0.037 | 0.0921 | 0.1036 | 0.0427 | 0.0111 | -0.0013 | 0.0361 | -0.0409 | -46.3603 | 23.1197 | -11.4877 | 17 | 3.3715 | -0.1835 | -0.0949 | 5.5399 | 0.5827 | 4.9567 | 0.0446 | 0.1039 | -0.055 | -0.061 | -0.2078 | 0.5567 | 0.0079 | -0.627 | 0.1633 | 0.0013 | 0.033 | -0.0111 | 0.2233 | -0.0783 | 0.0187 | -58.7583 | 10.772 | -20.406 | 18 | 6.2149 | 0.3645 | 0.9606 | 10.0957 | -1.0709 | 10.8114 | 0.0264 | -0.2468 | -0.1537 | 0.6999 | -0.1998 | 0.993 | 0.1937 | -0.9641 | 0.1733 | 0.1305 | -0.0579 | 0.067 | 0.4998 | -0.0985 | 0.2458 | -66.5433 | 6.1663 | -13.4224 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A46 - 64 | 2 | X-RAY DIFFRACTION | 2 | A65 - 129 | 3 | X-RAY DIFFRACTION | 3 | A130 - 215 | 4 | X-RAY DIFFRACTION | 4 | A216 - 268 | 5 | X-RAY DIFFRACTION | 5 | B30 - 42 | 6 | X-RAY DIFFRACTION | 6 | B43 - 72 | 7 | X-RAY DIFFRACTION | 7 | B73 - 119 | 8 | X-RAY DIFFRACTION | 8 | B120 - 205 | 9 | X-RAY DIFFRACTION | 9 | B206 - 246 | 10 | X-RAY DIFFRACTION | 10 | B247 - 258 | 11 | X-RAY DIFFRACTION | 11 | C45 - 64 | 12 | X-RAY DIFFRACTION | 12 | C65 - 130 | 13 | X-RAY DIFFRACTION | 13 | C131 - 206 | 14 | X-RAY DIFFRACTION | 14 | C207 - 268 | 15 | X-RAY DIFFRACTION | 15 | D33 - 72 | 16 | X-RAY DIFFRACTION | 16 | D73 - 176 | 17 | X-RAY DIFFRACTION | 17 | D177 - 218 | 18 | X-RAY DIFFRACTION | 18 | D219 - 254 | | | | | | | | | | | | | | | | | | |
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