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 | PHASER | | 位相決定 | XDS | | データ削減 | Coot | | モデル構築 | Blu-Ice | | データ収集 | XDS | | データスケーリング | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4K3D 解像度: 2.06→38.89 Å / SU ML: 0.31 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 29.67 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2347 | 2372 | 8.32 % |
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Rwork | 0.1941 | - | - |
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obs | 0.1975 | 28505 | 94.99 % |
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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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精密化ステップ | サイクル: LAST / 解像度: 2.06→38.89 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3556 | 0 | 0 | 55 | 3611 |
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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_d0.003 | 3648 | X-RAY DIFFRACTION | f_angle_d0.85 | 4964 | X-RAY DIFFRACTION | f_dihedral_angle_d12.99 | 1279 | X-RAY DIFFRACTION | f_chiral_restr0.03 | 580 | X-RAY DIFFRACTION | f_plane_restr0.003 | 632 | | | | | |
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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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2.0603-2.1023 | 0.4304 | 138 | 0.4257 | 1462 | X-RAY DIFFRACTION | 91 | 2.1023-2.1481 | 0.3125 | 142 | 0.3075 | 1561 | X-RAY DIFFRACTION | 99 | 2.1481-2.198 | 0.3193 | 140 | 0.2731 | 1598 | X-RAY DIFFRACTION | 99 | 2.198-2.253 | 0.3202 | 115 | 0.3073 | 1366 | X-RAY DIFFRACTION | 92 | 2.253-2.3139 | 0.2565 | 96 | 0.2639 | 1024 | X-RAY DIFFRACTION | 84 | 2.3139-2.382 | 0.308 | 147 | 0.2548 | 1585 | X-RAY DIFFRACTION | 99 | 2.382-2.4588 | 0.3229 | 149 | 0.2459 | 1586 | X-RAY DIFFRACTION | 98 | 2.4588-2.5467 | 0.3567 | 140 | 0.2617 | 1541 | X-RAY DIFFRACTION | 96 | 2.5467-2.6487 | 0.2992 | 141 | 0.251 | 1567 | X-RAY DIFFRACTION | 97 | 2.6487-2.7692 | 0.2481 | 149 | 0.2351 | 1601 | X-RAY DIFFRACTION | 99 | 2.7692-2.9151 | 0.2755 | 146 | 0.2222 | 1603 | X-RAY DIFFRACTION | 99 | 2.9151-3.0977 | 0.2712 | 142 | 0.2191 | 1595 | X-RAY DIFFRACTION | 99 | 3.0977-3.3367 | 0.2292 | 148 | 0.2035 | 1611 | X-RAY DIFFRACTION | 99 | 3.3367-3.6723 | 0.268 | 139 | 0.1878 | 1576 | X-RAY DIFFRACTION | 97 | 3.6723-4.2032 | 0.2146 | 143 | 0.1673 | 1603 | X-RAY DIFFRACTION | 97 | 4.2032-5.2934 | 0.1506 | 150 | 0.1374 | 1624 | X-RAY DIFFRACTION | 99 | 5.2934-38.8972 | 0.2132 | 147 | 0.1627 | 1630 | X-RAY DIFFRACTION | 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 | 2.8143 | -0.3407 | 0.1952 | 8.7156 | 0.0766 | 5.794 | -0.1956 | -0.3566 | -0.5516 | 0.8221 | 0.0827 | 0.5354 | 0.3176 | -0.3555 | 0.1013 | 0.4652 | 0.0547 | 0.0688 | 0.5671 | 0.104 | 0.5781 | 2.1383 | -38.927 | 31.4928 | 2 | 3.9104 | 0.1547 | 2.5203 | 0.374 | 1.0115 | 4.6591 | 0.2069 | -0.4728 | -0.2142 | -0.0654 | -0.139 | -0.2587 | 0.3269 | -0.6803 | -0.124 | 0.3815 | -0.0556 | 0.036 | 0.3701 | 0.0179 | 0.482 | -15.1501 | -40.6348 | 2.3064 | 3 | 3.4039 | 0.7831 | 0.5095 | 9.4447 | 0.5147 | 6.0162 | 0.178 | 0.1036 | -0.2284 | 0.244 | -0.3361 | -1.0439 | 0.1264 | 0.2179 | 0.1909 | 0.2513 | -0.0062 | -0.008 | 0.2591 | 0.027 | 0.5509 | -12.4909 | -42.0543 | -4.4291 | 4 | 3.4905 | 0.177 | 2.723 | 6.084 | -0.5748 | 5.6829 | -0.0794 | -0.4368 | 0.0843 | 0.8746 | 0.1298 | 0.3284 | -0.597 | -0.411 | -0.0255 | 0.4732 | 0.0954 | 0.073 | 0.52 | -0.0212 | 0.2717 | -0.2587 | -17.3728 | 26.5458 | 5 | 5.175 | -3.3966 | 2.4923 | 5.0277 | -3.0898 | 6.5682 | -0.9447 | -0.2163 | 1.0735 | 1.0487 | -0.0983 | 0.1014 | -1.7087 | 0.2574 | 1.0573 | 1.5858 | 0.0194 | -0.233 | 0.9118 | 0.0462 | 0.9946 | 21.0648 | -33.3006 | 58.5048 | 6 | 3.8981 | 1.5172 | 2.8005 | 2.0076 | 1.7308 | 4.9172 | 0.0981 | -0.0822 | -0.0939 | 0.1656 | 0.0387 | 0.2887 | 0.5685 | -0.0321 | -0.0918 | 0.3565 | 0.0885 | 0.1034 | 0.253 | 0.0237 | 0.3949 | -12.8294 | -28.7967 | 9.8775 | 7 | 7.3379 | -0.2298 | -0.4536 | 6.479 | 0.5561 | 4.6031 | -0.2366 | -0.2443 | -0.5135 | 0.4039 | -0.0653 | 0.7847 | 0.4058 | -0.152 | 0.2447 | 0.347 | -0.0065 | 0.0416 | 0.2727 | 0.0864 | 0.367 | -21.282 | -29.2156 | 5.337 |
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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 'L' and (resid 3 through 102 )2 | X-RAY DIFFRACTION | 2 | chain 'L' and (resid 103 through 128 )3 | X-RAY DIFFRACTION | 3 | chain 'L' and (resid 129 through 211 )4 | X-RAY DIFFRACTION | 4 | chain 'H' and (resid 1 through 100 )5 | X-RAY DIFFRACTION | 5 | chain 'H' and (resid 101 through 149 )6 | X-RAY DIFFRACTION | 6 | chain 'H' and (resid 150 through 200 )7 | X-RAY DIFFRACTION | 7 | chain 'H' and (resid 201 through 270 ) | | | | | | |
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