ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.2 | 精密化 | Aimless | | データスケーリング | XDS | | データ削減 | 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: 7XPT 解像度: 2.5→19.84 Å / SU ML: 0.31 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 37.18 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2956 | 1567 | 4.86 % |
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Rwork | 0.2565 | - | - |
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obs | 0.2583 | 32243 | 99.15 % |
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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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精密化ステップ | サイクル: LAST / 解像度: 2.5→19.84 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5777 | 0 | 2 | 131 | 5910 |
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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_d0.002 | 5925 | X-RAY DIFFRACTION | f_angle_d0.437 | 8093 | X-RAY DIFFRACTION | f_dihedral_angle_d12.445 | 2141 | X-RAY DIFFRACTION | f_chiral_restr0.04 | 892 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1088 | | | | | |
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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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2.5-2.58 | 0.3256 | 116 | 0.3373 | 2744 | X-RAY DIFFRACTION | 99 | 2.58-2.67 | 0.3426 | 139 | 0.3231 | 2759 | X-RAY DIFFRACTION | 99 | 2.67-2.78 | 0.3577 | 144 | 0.3012 | 2755 | X-RAY DIFFRACTION | 99 | 2.78-2.91 | 0.3357 | 150 | 0.2973 | 2756 | X-RAY DIFFRACTION | 100 | 2.91-3.06 | 0.3107 | 119 | 0.286 | 2804 | X-RAY DIFFRACTION | 99 | 3.06-3.25 | 0.3366 | 136 | 0.2913 | 2756 | X-RAY DIFFRACTION | 99 | 3.25-3.5 | 0.3503 | 158 | 0.2636 | 2768 | X-RAY DIFFRACTION | 99 | 3.5-3.85 | 0.3046 | 172 | 0.2459 | 2766 | X-RAY DIFFRACTION | 99 | 3.85-4.4 | 0.2607 | 115 | 0.2223 | 2842 | X-RAY DIFFRACTION | 100 | 4.4-5.52 | 0.2591 | 157 | 0.2198 | 2833 | X-RAY DIFFRACTION | 99 | 5.52-19.84 | 0.2376 | 161 | 0.2265 | 2893 | 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 | 2.7807 | -0.0466 | 0.334 | 3.1829 | 0.3664 | 2.7305 | -0.0476 | 0.7384 | 0.0287 | -0.8006 | 0.01 | -0.1082 | 0.2075 | 0.0134 | -0.0025 | 0.4831 | -0.0213 | -0.1221 | 0.5205 | -0.0595 | 0.3551 | 28.7625 | 14.0699 | -0.3666 | 2 | 1.4135 | -0.3782 | 0.5615 | 1.368 | 0.2734 | 0.7367 | -0.05 | 0.5828 | -0.1023 | -0.4307 | 0.0019 | 0.4158 | -0.1269 | 0.02 | -0.0796 | 0.398 | 0.0542 | -0.1115 | 0.2576 | 0.0325 | 0.4005 | 30.3921 | 19.9413 | 9.7249 | 3 | 2.0195 | 0.5141 | -0.007 | 3.3284 | 0.0255 | 0.9095 | -0.0029 | 0.0414 | -0.0449 | 0.1229 | 0.0212 | 0.4827 | 0.0097 | -0.0317 | 0.0181 | 0.3645 | 0.0089 | -0.1026 | 0.2995 | 0.0144 | 0.4852 | 22.5763 | 11.9607 | 24.9504 | 4 | 1.3238 | 0.1323 | 0.1159 | 0.7909 | -0.7544 | 0.9782 | 0.2273 | 0.2878 | 0.275 | -0.5539 | -0.0832 | 0.204 | -0.0329 | 0.045 | -0.0804 | 0.3133 | 0.0698 | -0.1056 | 0.2304 | -0.0592 | 0.6676 | 25.092 | 15.0835 | 20.7659 | 5 | 1.306 | 0.5165 | 0.9283 | 2.2601 | -0.1478 | 2.0101 | -0.0389 | -0.1609 | 0.0377 | 0.3254 | 0.0273 | -0.3285 | -0.2645 | -0.0421 | 0.012 | 0.3154 | 0.0234 | 0.0019 | 0.3489 | -0.047 | 0.5152 | 39.1419 | 16.2467 | 29.1759 | 6 | 1.5303 | -0.6241 | 0.5706 | 1.3752 | -0.0781 | 1.192 | 0.0132 | 0.457 | -0.0329 | -0.3922 | -0.0129 | -0.0664 | -0.2116 | 0.0866 | -0.0239 | 0.4852 | 0.0035 | 0.0097 | 0.401 | -0.0283 | 0.4841 | 20.9331 | 56.3121 | 8.0199 | 7 | 1.667 | 0.1583 | -0.4364 | 1.4546 | 0.1215 | 1.0786 | -0.0285 | 0.048 | -0.0723 | -0.122 | 0.0542 | -0.3169 | 0.0428 | 0.1007 | -0.0562 | 0.2819 | 0.0317 | -0.1127 | 0.25 | 0.0118 | 0.3679 | 19.6689 | 59.2165 | 25.6267 |
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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 4 through 56 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 57 through 138 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 139 through 258 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 259 through 293 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 294 through 374 )6 | X-RAY DIFFRACTION | 6 | chain 'C' and (resid 4 through 152 )7 | X-RAY DIFFRACTION | 7 | chain 'C' and (resid 153 through 374 ) | | | | | | |
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