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 | 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: 5WJM 解像度: 2.265→48.267 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.209 / SU B: 10.962 / SU ML: 0.139 / Average fsc free: 0.9114 / Average fsc work: 0.9292 / 交差検証法: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.194 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2517 | 1654 | 4.996 % |
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Rwork | 0.2087 | 31451 | - |
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all | 0.211 | - | - |
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obs | - | 33105 | 97.242 % |
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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: MASK BULK SOLVENT |
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原子変位パラメータ | Biso mean: 60.786 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.531 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -1.531 Å2 | 0 Å2 |
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3- | - | - | 3.061 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.265→48.267 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3270 | 0 | 6 | 104 | 3380 |
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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 | 3416 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.014 | 3200 | X-RAY DIFFRACTION | r_angle_refined_deg1.585 | 1.651 | 4687 | X-RAY DIFFRACTION | r_angle_other_deg1.235 | 1.577 | 7352 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.912 | 5 | 432 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg32.614 | 21.809 | 199 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.16 | 15 | 530 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg20.577 | 15 | 29 | X-RAY DIFFRACTION | r_chiral_restr0.068 | 0.2 | 471 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 3914 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 788 | X-RAY DIFFRACTION | r_nbd_refined0.198 | 0.2 | 527 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.175 | 0.2 | 2817 | X-RAY DIFFRACTION | r_nbtor_refined0.153 | 0.2 | 1554 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.072 | 0.2 | 1613 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.159 | 0.2 | 114 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.092 | 0.2 | 4 | X-RAY DIFFRACTION | r_metal_ion_refined0.086 | 0.2 | 26 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.172 | 0.2 | 11 | X-RAY DIFFRACTION | r_nbd_other0.188 | 0.2 | 56 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.277 | 0.2 | 5 | X-RAY DIFFRACTION | r_mcbond_it1.456 | 3.232 | 1689 | X-RAY DIFFRACTION | r_mcbond_other1.455 | 3.23 | 1688 | X-RAY DIFFRACTION | r_mcangle_it2.209 | 4.835 | 2107 | X-RAY DIFFRACTION | r_mcangle_other2.208 | 4.838 | 2108 | X-RAY DIFFRACTION | r_scbond_it1.73 | 3.47 | 1727 | X-RAY DIFFRACTION | r_scbond_other1.729 | 3.472 | 1728 | X-RAY DIFFRACTION | r_scangle_it2.761 | 5.128 | 2571 | X-RAY DIFFRACTION | r_scangle_other2.76 | 5.131 | 2572 | X-RAY DIFFRACTION | r_lrange_it4.431 | 37.021 | 3426 | X-RAY DIFFRACTION | r_lrange_other4.4 | 36.925 | 3414 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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2.265-2.324 | 0.347 | 118 | 0.291 | 2006 | X-RAY DIFFRACTION | 86.2713 | 2.324-2.388 | 0.332 | 111 | 0.274 | 2187 | X-RAY DIFFRACTION | 95.2736 | 2.388-2.457 | 0.313 | 120 | 0.242 | 2169 | X-RAY DIFFRACTION | 98.2825 | 2.457-2.533 | 0.305 | 109 | 0.228 | 2129 | X-RAY DIFFRACTION | 98.5035 | 2.533-2.616 | 0.271 | 101 | 0.215 | 2072 | X-RAY DIFFRACTION | 98.1925 | 2.616-2.707 | 0.282 | 118 | 0.212 | 1981 | X-RAY DIFFRACTION | 98.3138 | 2.707-2.809 | 0.25 | 100 | 0.208 | 1952 | X-RAY DIFFRACTION | 99.2263 | 2.809-2.924 | 0.279 | 101 | 0.209 | 1900 | X-RAY DIFFRACTION | 99.5027 | 2.924-3.054 | 0.254 | 101 | 0.212 | 1810 | X-RAY DIFFRACTION | 99.687 | 3.054-3.203 | 0.235 | 104 | 0.221 | 1714 | X-RAY DIFFRACTION | 99.8901 | 3.203-3.376 | 0.302 | 82 | 0.24 | 1694 | X-RAY DIFFRACTION | 99.8875 | 3.376-3.58 | 0.296 | 81 | 0.241 | 1573 | X-RAY DIFFRACTION | 99.8792 | 3.58-3.827 | 0.243 | 63 | 0.207 | 1502 | X-RAY DIFFRACTION | 99.8724 | 3.827-4.132 | 0.244 | 68 | 0.183 | 1406 | X-RAY DIFFRACTION | 99.7969 | 4.132-4.526 | 0.185 | 52 | 0.166 | 1295 | X-RAY DIFFRACTION | 98.8261 | 4.526-5.058 | 0.165 | 56 | 0.158 | 1174 | X-RAY DIFFRACTION | 98.6367 | 5.058-5.836 | 0.212 | 52 | 0.176 | 1004 | X-RAY DIFFRACTION | 95.7389 | 5.836-7.138 | 0.286 | 50 | 0.226 | 830 | X-RAY DIFFRACTION | 91.1917 | 7.138-10.056 | 0.195 | 43 | 0.186 | 653 | X-RAY DIFFRACTION | 91.3386 | 10.056-48.267 | 0.307 | 24 | 0.272 | 400 | X-RAY DIFFRACTION | 89.8305 |
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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 | 2.627 | -1.6275 | -0.3884 | 12.8782 | 4.685 | 4.4734 | -0.2786 | -0.7429 | 0.6362 | 1.3922 | 1.2426 | -2.4497 | 0.1478 | 0.8667 | -0.964 | 0.2105 | 0.1394 | -0.2953 | 0.478 | -0.4356 | 0.591 | 46.02 | 3.078 | 47.42 | 2 | 5.9166 | 2.2489 | 2.8549 | 1.9805 | 2.1663 | 4.1989 | -0.0569 | 0.2799 | 0.0316 | -0.1617 | 0.0388 | 0.065 | -0.0264 | -0.0206 | 0.0181 | 0.0383 | -0.0052 | 0.0042 | 0.0276 | -0.0061 | 0.026 | 18.455 | -20.528 | 14.194 | 3 | 13.2882 | -0.2593 | 7.0363 | 2.7993 | -2.2146 | 6.6666 | 1.0375 | -1.7766 | -2.0706 | 0.5132 | -0.032 | -0.2487 | 0.646 | -0.6631 | -1.0055 | 0.4603 | -0.1848 | -0.4083 | 0.4018 | 0.4301 | 0.8653 | 70.088 | -47.92 | 48.105 | 4 | 4.4035 | -0.4013 | 2.5618 | 2.6998 | -2.3907 | 5.2407 | 0.1781 | 0.1833 | -0.5359 | -0.2831 | -0.0684 | -0.2786 | 0.2454 | 0.1151 | -0.1097 | 0.0367 | 0.0143 | 0.0132 | 0.0699 | -0.0592 | 0.1399 | 41.099 | -29.324 | 10.608 |
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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 | ALLA1608 - 1714 | 2 | X-RAY DIFFRACTION | 1 | ALLA1901 - 1902 | 3 | X-RAY DIFFRACTION | 2 | ALLA1715 - 1822 | 4 | X-RAY DIFFRACTION | 2 | ALLA1903 | 5 | X-RAY DIFFRACTION | 3 | ALLB1607 - 1714 | 6 | X-RAY DIFFRACTION | 3 | ALLB1902 - 1903 | 7 | X-RAY DIFFRACTION | 4 | ALLB1715 - 1832 | 8 | X-RAY DIFFRACTION | 4 | ALLB1901 | | | | | | | | | | | | | | | | |
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