ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALEPACK | | データスケーリング | | PHENIX | 1.8_1063精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | HKL-2000 | | データ収集 | | HKL-2000 | | データ削減 | | SHARP | | 位相決定 | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.9→26.525 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8498 / SU ML: 0.23 / σ(F): 1.89 / 位相誤差: 22.72 / 立体化学のターゲット値: MLHL
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2145 | 3501 | 5.03 % |
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Rwork | 0.1802 | - | - |
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obs | 0.182 | 69605 | 98.49 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 121.11 Å2 / Biso mean: 35.3717 Å2 / Biso min: 11.24 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→26.525 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3595 | 0 | 0 | 169 | 3764 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.012 | 3712 | X-RAY DIFFRACTION | f_angle_d1.429 | 5060 | X-RAY DIFFRACTION | f_chiral_restr0.095 | 584 | X-RAY DIFFRACTION | f_plane_restr0.006 | 653 | X-RAY DIFFRACTION | f_dihedral_angle_d14.007 | 1346 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.9003-1.9263 | 0.3733 | 109 | 0.3098 | 2326 | 2435 | 87 | 1.9263-1.9538 | 0.3218 | 148 | 0.2585 | 2629 | 2777 | 97 | 1.9538-1.983 | 0.2586 | 159 | 0.2471 | 2596 | 2755 | 99 | 1.983-2.0139 | 0.2882 | 152 | 0.2307 | 2666 | 2818 | 98 | 2.0139-2.047 | 0.2529 | 126 | 0.2189 | 2659 | 2785 | 99 | 2.047-2.0822 | 0.2855 | 137 | 0.1996 | 2628 | 2765 | 99 | 2.0822-2.1201 | 0.2538 | 121 | 0.2 | 2668 | 2789 | 98 | 2.1201-2.1608 | 0.2664 | 147 | 0.2031 | 2636 | 2783 | 99 | 2.1608-2.2049 | 0.2416 | 116 | 0.2007 | 2669 | 2785 | 99 | 2.2049-2.2528 | 0.2402 | 141 | 0.2003 | 2644 | 2785 | 99 | 2.2528-2.3052 | 0.2938 | 100 | 0.1929 | 2693 | 2793 | 99 | 2.3052-2.3628 | 0.2232 | 131 | 0.1987 | 2694 | 2825 | 99 | 2.3628-2.4267 | 0.2402 | 155 | 0.1963 | 2691 | 2846 | 100 | 2.4267-2.498 | 0.2247 | 121 | 0.1866 | 2656 | 2777 | 99 | 2.498-2.5786 | 0.2222 | 158 | 0.1888 | 2676 | 2834 | 99 | 2.5786-2.6707 | 0.2234 | 147 | 0.1867 | 2643 | 2790 | 99 | 2.6707-2.7775 | 0.2329 | 161 | 0.1866 | 2691 | 2852 | 99 | 2.7775-2.9038 | 0.254 | 146 | 0.1869 | 2622 | 2768 | 99 | 2.9038-3.0566 | 0.179 | 140 | 0.1835 | 2671 | 2811 | 100 | 3.0566-3.2478 | 0.2217 | 202 | 0.185 | 2612 | 2814 | 100 | 3.2478-3.4981 | 0.1939 | 136 | 0.173 | 2683 | 2819 | 100 | 3.4981-3.8492 | 0.1956 | 137 | 0.168 | 2651 | 2788 | 100 | 3.8492-4.404 | 0.1725 | 123 | 0.1459 | 2720 | 2843 | 99 | 4.404-5.5402 | 0.175 | 142 | 0.1433 | 2659 | 2801 | 99 | 5.5402-26.5272 | 0.1896 | 146 | 0.1722 | 2621 | 2767 | 98 |
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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 | 3.0567 | -0.3412 | -0.9093 | 6.2797 | -2.2024 | 3.4068 | -0.0068 | -0.0335 | 0.1315 | 0.102 | -0.1166 | -0.2885 | -0.1474 | 0.4362 | 0.1063 | 0.1597 | -0.0357 | 0.0159 | 0.3612 | -0.112 | 0.2464 | 47.8877 | -2.95 | 8.4705 | 2 | 3.3911 | -1.7461 | -0.7075 | 2.5268 | -0.3593 | 2.6154 | 0.135 | 0.5127 | 0.2194 | -0.3272 | 0.1168 | -0.3657 | -0.4674 | 0.2187 | -0.1602 | 0.2392 | -0.0809 | 0.0605 | 0.2633 | -0.0109 | 0.2108 | 38.2717 | 10.1284 | 6.1218 | 3 | 2.2615 | 0.3836 | -0.0103 | 2.4528 | 0.1118 | 1.8857 | 0.0198 | 0.3703 | 0.3992 | -0.1711 | 0.0402 | 0.0793 | -0.4099 | -0.0899 | -0.0375 | 0.2477 | 0.0047 | 0.0116 | 0.1597 | 0.0676 | 0.2146 | 23.2931 | 14.1879 | 12.8916 | 4 | 3.592 | -0.6508 | 0.0475 | 2.876 | -0.1498 | 2.8124 | -0.0608 | 0.1353 | 0.0284 | 0.1119 | 0.0087 | 0.1927 | -0.1345 | -0.0474 | 0.0337 | 0.1669 | -0.0368 | -0.0037 | 0.1297 | 0.0139 | 0.134 | 25.4695 | -5.9082 | 24.4898 | 5 | 3.0247 | 0.2948 | -1.8578 | 1.5703 | -0.2982 | 2.0744 | -0.2989 | -0.2254 | -0.564 | 0.0225 | 0.0746 | -0.2301 | 0.4008 | 0.4161 | 0.149 | 0.2262 | 0.0247 | -0.011 | 0.2666 | 0.001 | 0.275 | 37.6658 | -18.1731 | 20.6869 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 3 through 58 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 59 through 131 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 132 through 248 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 249 through 387 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 388 through 493 )A0 | | | | | | | | | | |
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