ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | | 精密化 | PDB_EXTRACT | 3.15 | データ抽出 | HKL-2000 | | データ削減 | SCALEPACK | | データスケーリング | PHENIX | | 位相決定 |
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精密化 | 解像度: 1.835→31.827 Å / FOM work R set: 0.8683 / SU ML: 0.17 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 19.68 / 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 | 0.2013 | 1998 | 3.06 % | random selection |
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Rwork | 0.1671 | 63363 | - | - |
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obs | 0.1682 | 65361 | 99.57 % | - |
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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: 93.63 Å2 / Biso mean: 19.62 Å2 / Biso min: 2.77 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.835→31.827 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4730 | 0 | 19 | 819 | 5568 |
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Biso mean | - | - | 22.35 | 30.36 | - |
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残基数 | - | - | - | - | 584 |
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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_d0.006 | 4905 | X-RAY DIFFRACTION | f_angle_d0.925 | 6669 | X-RAY DIFFRACTION | f_chiral_restr0.037 | 678 | X-RAY DIFFRACTION | f_plane_restr0.004 | 869 | X-RAY DIFFRACTION | f_dihedral_angle_d12.896 | 1744 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8352-1.8811 | 0.2651 | 125 | 0.2011 | 4374 | 4499 | 97 | 1.8811-1.9319 | 0.2608 | 155 | 0.1864 | 4484 | 4639 | 100 | 1.9319-1.9888 | 0.2251 | 135 | 0.181 | 4492 | 4627 | 100 | 1.9888-2.053 | 0.215 | 140 | 0.1709 | 4506 | 4646 | 100 | 2.053-2.1263 | 0.207 | 143 | 0.164 | 4460 | 4603 | 100 | 2.1263-2.2114 | 0.1792 | 149 | 0.17 | 4514 | 4663 | 100 | 2.2114-2.3121 | 0.2131 | 139 | 0.166 | 4510 | 4649 | 100 | 2.3121-2.4339 | 0.2116 | 146 | 0.1694 | 4521 | 4667 | 100 | 2.4339-2.5863 | 0.2299 | 140 | 0.175 | 4545 | 4685 | 100 | 2.5863-2.7859 | 0.2498 | 139 | 0.1773 | 4542 | 4681 | 100 | 2.7859-3.0661 | 0.1675 | 146 | 0.1714 | 4543 | 4689 | 100 | 3.0661-3.5093 | 0.2208 | 146 | 0.165 | 4570 | 4716 | 100 | 3.5093-4.4194 | 0.1505 | 142 | 0.1451 | 4613 | 4755 | 100 | 4.4194-31.8317 | 0.1909 | 153 | 0.1647 | 4689 | 4842 | 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 | -0.0031 | -0.0046 | 0.0017 | -0.0026 | -0.0031 | 0.0001 | -0.0419 | 0.0147 | 0.0184 | -0.0077 | -0.017 | -0.0112 | -0.023 | 0.0024 | 0 | 0.0341 | 0.0423 | -0.0595 | -0.0334 | 0.041 | -0.0036 | 91.4523 | 46.2005 | 58.071 | 2 | -0.0016 | 0.0002 | -0.0028 | 0.0006 | -0.0008 | -0.0009 | -0.0126 | -0.0237 | 0.0168 | 0.0201 | -0.014 | 0.0016 | -0.0203 | -0.0102 | 0 | 0.0673 | 0.0598 | -0.0795 | -0.0341 | 0.0262 | 0.0638 | 89.7668 | 55.8324 | 77.9771 | 3 | 0.0012 | -0.001 | 0.0019 | -0.0045 | -0.002 | 0.0018 | -0.0351 | -0.0162 | 0.0194 | 0.0193 | -0.0174 | 0.0032 | -0.0327 | 0.0043 | 0 | -0.093 | 0.0504 | -0.1227 | -0.0131 | 0.0486 | -0.0917 | 98.5015 | 44.8934 | 77.7334 | 4 | 0.0085 | 0.0112 | 0.0055 | 0.0163 | 0.0081 | 0.0346 | -0.0075 | -0.0239 | -0.0044 | -0.0041 | -0.0144 | 0.0002 | -0.0002 | -0.0487 | 0 | 0.0551 | 0.016 | -0.0093 | 0.0663 | -0.011 | 0.0534 | 79.4631 | 28.9016 | 60.5045 | 5 | 0.0036 | 0.0017 | -0.0061 | 0.0044 | -0.0102 | 0.0084 | -0.0109 | 0.0156 | -0.0077 | -0.0021 | -0.0201 | -0.0057 | -0.0277 | 0.0222 | -0 | 0.0456 | -0.001 | -0.0058 | 0.052 | 0.0063 | 0.0411 | 99.4479 | 35.3148 | 53.5432 |
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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 | chain 'A' and (resid 46 through 104 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 105 through 158 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 159 through 250 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 251 through 576 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 577 through 642 )A0 | | | | | | | | | | |
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