ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.17.1_3660精密化 | XDS | | データ削減 | XDS | | 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: 2.04→44.26 Å / SU ML: 0.2785 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 27.596 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2271 | 1262 | 5 % |
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Rwork | 0.1778 | 23989 | - |
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obs | 0.1802 | 25251 | 96.74 % |
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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 mean: 46.68 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.04→44.26 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3464 | 0 | 1 | 143 | 3608 |
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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_d0.0146 | 3565 | X-RAY DIFFRACTION | f_angle_d1.0991 | 4861 | X-RAY DIFFRACTION | f_chiral_restr0.0619 | 545 | X-RAY DIFFRACTION | f_plane_restr0.008 | 636 | X-RAY DIFFRACTION | f_dihedral_angle_d14.7957 | 1255 | | | | | |
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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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2.04-2.13 | 0.3712 | 114 | 0.3223 | 2165 | X-RAY DIFFRACTION | 78.61 | 2.13-2.22 | 0.3502 | 135 | 0.2743 | 2559 | X-RAY DIFFRACTION | 93.38 | 2.22-2.34 | 0.2728 | 143 | 0.2312 | 2717 | X-RAY DIFFRACTION | 99.31 | 2.34-2.49 | 0.2487 | 144 | 0.2066 | 2730 | X-RAY DIFFRACTION | 99.93 | 2.49-2.68 | 0.2498 | 144 | 0.1866 | 2736 | X-RAY DIFFRACTION | 99.86 | 2.68-2.95 | 0.2699 | 144 | 0.1923 | 2744 | X-RAY DIFFRACTION | 99.86 | 2.95-3.37 | 0.2183 | 144 | 0.1823 | 2759 | X-RAY DIFFRACTION | 99.93 | 3.37-4.25 | 0.1885 | 146 | 0.1537 | 2769 | X-RAY DIFFRACTION | 99.9 | 4.25-44.26 | 0.2005 | 148 | 0.1459 | 2810 | X-RAY DIFFRACTION | 99.83 |
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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 | 0.262047393702 | -0.0405096017959 | 0.159637166663 | 0.399094268766 | -0.130847351127 | 0.963654101308 | -0.00832119548171 | -0.167852139659 | -0.0745169677174 | -0.0478103982147 | 0.0133663983325 | 0.0442097615648 | 0.0801051176581 | -0.0230545145334 | 2.91607512488E-6 | 0.340278496998 | -0.0023997720864 | 0.000442151785409 | 0.439628905811 | -0.00962314901086 | 0.401521562058 | 10.7167492444 | 33.5513743381 | 17.1571094496 | 2 | 0.916009784346 | -0.545558415136 | 0.0237294512861 | 0.387022504205 | 0.11215750403 | 0.420744789551 | -0.353053194676 | -0.187747110783 | -0.049637464132 | 0.147280606235 | -0.156880321895 | -0.0607852068082 | -0.437685712572 | -0.436550385945 | -0.127460956507 | 0.351754574643 | 0.0351184921931 | 0.0214742999164 | 0.501137152699 | -0.0829672925152 | 0.464853483143 | 11.6691686158 | 45.1629359377 | 15.8115884353 | 3 | 0.581898376947 | 0.29041447437 | -0.212607937735 | 0.653378901942 | 0.0672073964008 | 1.32012058565 | -0.0100145674096 | 0.0512232675283 | 0.0384756020386 | -0.0890958253492 | 0.0205369322137 | -0.0241719241079 | 0.00578378720541 | 0.00570547069197 | 2.03837779667E-7 | 0.360158364319 | -0.0162727412306 | -0.00688997018848 | 0.324875150962 | -0.0054462045494 | 0.350623167696 | 10.9051512766 | 38.4244230426 | -5.46152276124 |
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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 11 through 236 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 237 through 265 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 266 through 474 ) | | |
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