ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.20.1_4487精密化 | XDS | | データ削減 | XSCALE | | 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 / 解像度: 1.73→35.87 Å / SU ML: 0.2373 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 23.6134 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2117 | 2007 | 4.81 % |
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Rwork | 0.1753 | 39760 | - |
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obs | 0.1771 | 41767 | 99.29 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso mean: 35.34 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.73→35.87 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3240 | 0 | 14 | 296 | 3550 |
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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_d0.0094 | 3344 | X-RAY DIFFRACTION | f_angle_d0.9201 | 4567 | X-RAY DIFFRACTION | f_chiral_restr0.0609 | 536 | X-RAY DIFFRACTION | f_plane_restr0.0078 | 574 | X-RAY DIFFRACTION | f_dihedral_angle_d12.8126 | 1194 | | | | | |
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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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1.73-1.77 | 0.3906 | 140 | 0.3143 | 2799 | X-RAY DIFFRACTION | 99.22 | 1.77-1.82 | 0.2739 | 144 | 0.2546 | 2841 | X-RAY DIFFRACTION | 99.24 | 1.82-1.87 | 0.2655 | 142 | 0.2352 | 2783 | X-RAY DIFFRACTION | 98.42 | 1.87-1.94 | 0.2932 | 144 | 0.2258 | 2853 | X-RAY DIFFRACTION | 99.34 | 1.94-2 | 0.2393 | 144 | 0.1829 | 2795 | X-RAY DIFFRACTION | 99.59 | 2-2.08 | 0.2436 | 139 | 0.1819 | 2862 | X-RAY DIFFRACTION | 99.54 | 2.08-2.18 | 0.2092 | 143 | 0.1782 | 2887 | X-RAY DIFFRACTION | 99.64 | 2.18-2.29 | 0.227 | 141 | 0.1836 | 2833 | X-RAY DIFFRACTION | 99.56 | 2.29-2.44 | 0.2048 | 145 | 0.1797 | 2851 | X-RAY DIFFRACTION | 99.83 | 2.44-2.63 | 0.2393 | 144 | 0.1811 | 2789 | X-RAY DIFFRACTION | 97.83 | 2.63-2.89 | 0.2088 | 147 | 0.1858 | 2858 | X-RAY DIFFRACTION | 99.83 | 2.89-3.31 | 0.1788 | 140 | 0.1729 | 2871 | X-RAY DIFFRACTION | 99.93 | 3.31-4.17 | 0.1953 | 147 | 0.1524 | 2857 | X-RAY DIFFRACTION | 99.4 | 4.17-35.87 | 0.1889 | 147 | 0.1532 | 2881 | X-RAY DIFFRACTION | 98.66 |
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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 | 2.15869902608 | -0.282454521749 | -0.237602503183 | 2.34017350614 | -0.52665572836 | 2.34207658559 | -0.0987006739812 | -0.148225002965 | 0.101191261385 | 0.0328085184697 | 0.0788519926895 | 0.104412503428 | 0.0882341707105 | -0.0360749979951 | 1.85198052941 | 0.145924622669 | 0.0112237627142 | 0.00354042819245 | 0.131525307679 | -0.0166626887353 | 0.187024290772 | -19.998 | 4.626 | 4.353 | 2 | 3.55944298472 | -1.07980207435 | 0.400527897298 | 2.76099908509 | -0.307065501583 | 3.31416469853 | -0.128054645349 | -0.699408099676 | 0.0446801683179 | 0.122376447406 | 0.18706680068 | -0.10647646485 | -0.547532204968 | 0.255765502685 | -0.0405671440292 | 0.326902891869 | -0.0562971968318 | -0.0232685187807 | 0.428149364481 | -0.0088808900076 | 0.183784850444 | -8.734 | -11.956 | 28.453 | 3 | 2.34128286764 | -1.32784877453 | 0.362161851506 | 3.73055630865 | -0.685659012879 | 1.1492845917 | 0.0390324059524 | 0.104333722636 | -0.0852810329821 | -0.225907156244 | -0.00949508637728 | 0.0005542681457 | 0.013514076579 | 0.0096688283465 | -0.0262980981611 | 0.207030418105 | -0.0229360956743 | 0.00654326248964 | 0.153994693554 | -0.0198470460117 | 0.165318299165 | -11.12 | -12.679 | -6.869 | 4 | 1.66724289625 | -0.862259082658 | -0.981675909646 | 1.6258224973 | 1.09456726458 | 4.46732813452 | -0.127543621721 | -0.639489969559 | -0.28180503898 | 0.289942475472 | 0.187697030147 | 0.238067438741 | 0.369991415902 | 0.0914082749055 | -0.0530611434934 | 0.242225579883 | -0.0029951150897 | -0.0177689011678 | 0.437541754248 | 0.114683442078 | 0.243848002285 | -13.391 | -27.718 | 27.151 |
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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 H AND RESID 1:119 )H1 - 119 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN H AND RESID 120:214 )H120 - 214 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN L AND RESID 1:107 )L1 - 107 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN L AND RESID 108:212 )L108 - 212 | | | | | | | | |
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