ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.21_5207: ???)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: 3→44.66 Å / SU ML: 0.45 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 30.49 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2966 | 1445 | 10.03 % |
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Rwork | 0.2497 | - | - |
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obs | 0.2545 | 14404 | 93.95 % |
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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: 3→44.66 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5451 | 0 | 62 | 0 | 5513 |
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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_d0.005 | 5647 | X-RAY DIFFRACTION | f_angle_d1.034 | 7706 | X-RAY DIFFRACTION | f_dihedral_angle_d14.385 | 1996 | X-RAY DIFFRACTION | f_chiral_restr0.061 | 858 | X-RAY DIFFRACTION | f_plane_restr0.012 | 999 | | | | | |
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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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3-3.11 | 0.3386 | 136 | 0.2997 | 1226 | X-RAY DIFFRACTION | 91 | 3.11-3.23 | 0.3316 | 134 | 0.2881 | 1284 | X-RAY DIFFRACTION | 94 | 3.23-3.38 | 0.301 | 150 | 0.2803 | 1301 | X-RAY DIFFRACTION | 96 | 3.38-3.56 | 0.3213 | 149 | 0.2561 | 1307 | X-RAY DIFFRACTION | 96 | 3.56-3.78 | 0.3449 | 142 | 0.249 | 1283 | X-RAY DIFFRACTION | 95 | 3.78-4.07 | 0.2666 | 149 | 0.2324 | 1304 | X-RAY DIFFRACTION | 95 | 4.07-4.48 | 0.275 | 148 | 0.2297 | 1298 | X-RAY DIFFRACTION | 94 | 4.48-5.13 | 0.2549 | 143 | 0.2282 | 1309 | X-RAY DIFFRACTION | 94 | 5.13-6.46 | 0.3301 | 140 | 0.2553 | 1301 | X-RAY DIFFRACTION | 92 | 6.46-44.66 | 0.2762 | 154 | 0.2391 | 1346 | X-RAY DIFFRACTION | 91 |
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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 | 0.1651 | -0.0831 | -0.0206 | 0.4887 | -0.3647 | 0.4243 | 0.0357 | -0.2546 | -0.1112 | 0.2372 | -0.0706 | 0.0052 | 0.078 | 0.0206 | 0.0913 | 0.32 | 0.0046 | 0.0182 | 0.2831 | 0.029 | 0.3279 | 3.3783 | 17.7399 | 14.7122 | 2 | 0.9753 | -0.5079 | 0.8595 | 1.0287 | -0.6151 | 0.7922 | -0.0269 | 0.0797 | 0.1355 | 0.1522 | -0.0255 | 0.0458 | -0.1003 | 0.0767 | -0.0981 | 0.3226 | -0.0448 | 0.0739 | 0.219 | -0.0391 | 0.3205 | 7.7379 | 28.6074 | 28.0175 | 3 | 0.4441 | -0.2206 | -0.3337 | 0.9126 | 0.163 | 0.6898 | 0.0535 | 0.1254 | -0.2403 | 0.0822 | -0.2785 | 0.0935 | 0.0271 | 0.1389 | -0.0897 | 0.2741 | -0.0339 | -0.0293 | 0.3955 | 0.0969 | 0.324 | -8.5395 | 26.5865 | 12.9854 | 4 | 0.0938 | -0.0876 | 0.2984 | 0.0767 | -0.2239 | 1.241 | -0.0253 | 0.0829 | 0.13 | -0.1134 | -0.0107 | 0.1945 | 0.2101 | 0.227 | 0.1324 | 0.3232 | -0.0674 | 0.0441 | 0.1975 | 0.0595 | 0.3521 | 46.4599 | 28.6456 | 33.8855 | 5 | 1.1012 | -0.3325 | 0.6941 | 1.1677 | 0.0317 | 1.9008 | 0.1762 | 0.139 | 0.0845 | -0.1623 | -0.1768 | -0.3789 | -0.192 | 0.4008 | -0.1673 | 0.2476 | -0.0421 | 0.0398 | 0.1701 | -0.0263 | 0.3174 | 51.8142 | 27.2012 | 16.4951 | 6 | 0.5112 | 0.3634 | -0.115 | 2.1182 | 0.2181 | 0.2457 | 0.0601 | 0.0536 | -0.4428 | -0.6076 | 0.1508 | -0.1961 | -0.2573 | 0.1722 | 0.2353 | 0.3764 | 0.0676 | -0.042 | 0.273 | -0.0045 | 0.2988 | 52.9774 | 15.726 | 20.5914 | 7 | 1.2854 | -0.4297 | 1.0458 | 0.8098 | -0.0303 | 2.0421 | 0.1495 | 0.2888 | 0.0724 | 0.0255 | -0.0369 | -0.1154 | 0.1379 | 0.2063 | 0.1138 | 0.358 | -0.0505 | -0.019 | 0.1351 | 0.0004 | 0.3024 | 45.1836 | 9.656 | 26.1903 | 8 | 1.4403 | -0.0361 | -0.4059 | 1.1609 | 0.1981 | 0.8988 | 0.2057 | 0.2704 | 0.1376 | -0.1178 | -0.3176 | 0.1711 | 0.1625 | -0.3574 | -0.0658 | 0.3741 | -0.0728 | -0.045 | 0.2833 | 0.0252 | 0.2752 | 32.4241 | 23.7216 | 36.389 |
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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 10 through 122 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 123 through 270 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 271 through 384 )4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 10 through 122 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 123 through 176 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 177 through 229 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 230 through 311 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 312 through 384 ) | | | | | | | |
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