ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.9_1692精密化 | MOSFLM | | データ削減 | SCALA | | 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: 2ccm 解像度: 2.201→27.353 Å / SU ML: 0.7 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 44.09 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.3044 | 870 | 5.13 % |
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Rwork | 0.215 | - | - |
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obs | 0.2193 | 9020 | 99.47 % |
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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 mean: 61.5 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.201→27.353 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1522 | 0 | 3 | 30 | 1555 |
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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_d0.009 | 1596 | X-RAY DIFFRACTION | f_angle_d1.058 | 2131 | X-RAY DIFFRACTION | f_dihedral_angle_d16.69 | 577 | X-RAY DIFFRACTION | f_chiral_restr0.04 | 219 | X-RAY DIFFRACTION | f_plane_restr0.004 | 274 | | | | | |
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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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2.2006-2.3384 | 0.4675 | 128 | 0.3962 | 2677 | X-RAY DIFFRACTION | 99 | 2.3384-2.5188 | 0.4218 | 155 | 0.3845 | 2651 | X-RAY DIFFRACTION | 99 | 2.5188-2.7721 | 0.3675 | 165 | 0.3197 | 2676 | X-RAY DIFFRACTION | 100 | 2.7721-3.1727 | 0.3701 | 160 | 0.2579 | 2704 | X-RAY DIFFRACTION | 100 | 3.1727-3.9952 | 0.2765 | 134 | 0.1796 | 2686 | X-RAY DIFFRACTION | 100 | 3.9952-27.3548 | 0.2245 | 128 | 0.141 | 2706 | X-RAY DIFFRACTION | 99 |
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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 | 4.6202 | -2.2682 | -1.0963 | 2.5302 | 0.8559 | 4.7411 | -0.6261 | -0.0716 | -1.0973 | -0.0199 | 1.3068 | 0.0297 | -0.0596 | 0.2689 | 0.3573 | 0.5043 | -0.1099 | 0.1757 | 0.929 | -0.5672 | 0.2958 | -9.039 | 16.7761 | 9.1926 | 2 | 0.8671 | -0.059 | 1.7753 | 2.2334 | 0.3349 | 3.6487 | 0.3396 | -0.6538 | 0.7073 | -0.007 | -0.0811 | 0.3011 | -0.3804 | -0.7045 | -0.2752 | 0.412 | -0.0283 | 0.2801 | 0.6531 | -0.2539 | 0.7467 | -28.1023 | 24.8942 | 7.4471 | 3 | 3.9868 | -0.3334 | 0.9817 | 4.9957 | -0.7703 | 4.8077 | 0.5883 | -0.1194 | -0.6322 | -0.0924 | -0.0468 | 0.6928 | 0.3695 | 0.1138 | -0.4086 | 0.3368 | -0.0661 | 0.0769 | 0.3864 | -0.1756 | 0.5254 | -22.3841 | 12.5295 | 3.1352 | 4 | 5.7007 | -0.5428 | -0.1024 | 1.8938 | -2.1131 | 6.4851 | -0.0036 | -0.3568 | -0.4428 | 0.1164 | 0.8158 | 0.5126 | 0.4558 | 0.9671 | -0.6043 | 0.3959 | -0.0336 | 0.1447 | 0.5086 | -0.1992 | 0.7343 | -17.8192 | 18.3235 | -4.9187 | 5 | 2.9774 | -0.8946 | 0.6391 | 1.9767 | 0.0451 | 3.1519 | 0.3528 | -0.1056 | 0.5384 | -0.0521 | 0.4058 | -0.3716 | -0.7071 | 0.7871 | -0.5926 | 0.5351 | -0.176 | 0.3157 | 0.725 | -0.4018 | 0.9167 | -9.8323 | 29.9948 | -1.1894 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 5 through 21 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 22 through 52 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 53 through 98 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 99 through 118 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 119 through 189 ) | | | | |
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