ソフトウェア | 名称 | バージョン | 分類 | NB |
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PHENIX | 1.8.2_1309精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | MxCuBE | | データ収集 | | XDS | | データ削減 | | XSCALE | | データスケーリング | | MOLREP | | 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: 2.5→43.55 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6963 / SU ML: 0.52 / σ(F): 1.18 / 位相誤差: 35.8 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2535 | 1759 | 3.59 % | Random |
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Rwork | 0.205 | 88457 | - | - |
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obs | 0.2068 | 48932 | 83.12 % | - |
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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 max: 193.4 Å2 / Biso mean: 94.3173 Å2 / Biso min: 38.98 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.5→43.55 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 9524 | 0 | 291 | 47 | 9862 |
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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_d0.008 | 10064 | X-RAY DIFFRACTION | f_angle_d1.101 | 13639 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 1438 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1717 | X-RAY DIFFRACTION | f_dihedral_angle_d13.804 | 3645 | | | | | |
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Refine LS restraints NCS | 数: 5794 / タイプ: POSITIONAL / Rms dev position: 7.497 Å |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.5-2.5357 | 0.4133 | 57 | 0.4501 | 1669 | 1726 | 38 | 2.5357-2.5735 | 0.4989 | 84 | 0.4552 | 1877 | 1961 | 43 | 2.5735-2.6138 | 0.4347 | 94 | 0.406 | 2110 | 2204 | 47 | 2.6138-2.6566 | 0.448 | 88 | 0.3982 | 2359 | 2447 | 54 | 2.6566-2.7024 | 0.4255 | 82 | 0.3977 | 2649 | 2731 | 59 | 2.7024-2.7515 | 0.3125 | 104 | 0.3987 | 2859 | 2963 | 66 | 2.7515-2.8044 | 0.4171 | 117 | 0.4013 | 3203 | 3320 | 71 | 2.8044-2.8617 | 0.4548 | 142 | 0.3845 | 3420 | 3562 | 77 | 2.8617-2.9239 | 0.4314 | 129 | 0.3386 | 3613 | 3742 | 83 | 2.9239-2.9919 | 0.4304 | 154 | 0.3079 | 4042 | 4196 | 90 | 2.9919-3.0667 | 0.3819 | 159 | 0.3038 | 4304 | 4463 | 97 | 3.0667-3.1496 | 0.2928 | 159 | 0.2846 | 4357 | 4516 | 98 | 3.1496-3.2422 | 0.3459 | 161 | 0.2718 | 4362 | 4523 | 98 | 3.2422-3.3468 | 0.368 | 165 | 0.2586 | 4364 | 4529 | 98 | 3.3468-3.4664 | 0.3619 | 161 | 0.2512 | 4327 | 4488 | 98 | 3.4664-3.6051 | 0.3177 | 163 | 0.2003 | 4378 | 4541 | 98 | 3.6051-3.7691 | 0.2172 | 159 | 0.177 | 4397 | 4556 | 98 | 3.7691-3.9677 | 0.2515 | 159 | 0.1631 | 4313 | 4472 | 98 | 3.9677-4.2161 | 0.1653 | 160 | 0.1411 | 4357 | 4517 | 98 | 4.2161-4.5413 | 0.2136 | 161 | 0.1205 | 4334 | 4495 | 98 | 4.5413-4.9978 | 0.1596 | 160 | 0.1303 | 4345 | 4505 | 97 | 4.9978-5.7196 | 0.2309 | 155 | 0.1494 | 4280 | 4435 | 97 | 5.7196-7.2008 | 0.1907 | 160 | 0.1918 | 4282 | 4442 | 97 | 7.2008-43.5599 | 0.1639 | 157 | 0.159 | 4256 | 4413 | 95 |
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精密化 TLS | 手法: refined / Origin x: 8.3077 Å / Origin y: -0.2467 Å / Origin z: 29.0052 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.6298 Å2 | -0.0515 Å2 | -0.1215 Å2 | - | 0.4143 Å2 | 0.0128 Å2 | - | - | 0.3242 Å2 |
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L | 1.0437 °2 | -0.1241 °2 | 0.1987 °2 | - | 1.0872 °2 | 0.213 °2 | - | - | 1.2742 °2 |
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S | -0.0895 Å ° | -0.0838 Å ° | 0.154 Å ° | 0.2121 Å ° | -0.059 Å ° | -0.0375 Å ° | -0.0723 Å ° | 0.0347 Å ° | 0.1447 Å ° |
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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 | allA4 - 239 | 2 | X-RAY DIFFRACTION | 1 | allB0 - 239 | 3 | X-RAY DIFFRACTION | 1 | allC4 - 239 | 4 | X-RAY DIFFRACTION | 1 | allD4 - 239 | 5 | X-RAY DIFFRACTION | 1 | allE0 - 239 | 6 | X-RAY DIFFRACTION | 1 | allS3 - 75 | 7 | X-RAY DIFFRACTION | 1 | allF1 | 8 | X-RAY DIFFRACTION | 1 | allN1 | 9 | X-RAY DIFFRACTION | 1 | allP1 | 10 | X-RAY DIFFRACTION | 1 | allT1 | 11 | X-RAY DIFFRACTION | 1 | allK1 | 12 | X-RAY DIFFRACTION | 1 | allU1 | 13 | X-RAY DIFFRACTION | 1 | allQ1 | 14 | X-RAY DIFFRACTION | 1 | allV1 | 15 | X-RAY DIFFRACTION | 1 | allL1 | 16 | X-RAY DIFFRACTION | 1 | allR1 | 17 | X-RAY DIFFRACTION | 1 | allM1 | 18 | X-RAY DIFFRACTION | 1 | allW1 | 19 | X-RAY DIFFRACTION | 1 | allX1 | 20 | X-RAY DIFFRACTION | 1 | allY1 | 21 | X-RAY DIFFRACTION | 1 | allZ1 | 22 | X-RAY DIFFRACTION | 1 | alla1 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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