ソフトウェア | 名称 | バージョン | 分類 |
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MxCuBE | 3 | データ収集 | PHENIX | 1.19.2_4158精密化 | xia2 | | データ削減 | Coot | | モデル構築 | 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: 6YWF 解像度: 1.51→19.05 Å / SU ML: 0.156 / 交差検証法: FREE R-VALUE / σ(F): 1.99 / 位相誤差: 24.1936 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 | 0.1988 | 1458 | 5.1 % |
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Rwork | 0.1692 | 27126 | - |
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obs | 0.1707 | 28584 | 90.86 % |
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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: 17.74 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.51→19.05 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1737 | 0 | 78 | 217 | 2032 |
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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 | 1902 | X-RAY DIFFRACTION | f_angle_d1.1188 | 2603 | X-RAY DIFFRACTION | f_chiral_restr0.0615 | 311 | X-RAY DIFFRACTION | f_plane_restr0.0094 | 332 | X-RAY DIFFRACTION | f_dihedral_angle_d13.6785 | 642 | | | | | |
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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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1.51-1.56 | 0.2972 | 127 | 0.2442 | 2420 | X-RAY DIFFRACTION | 80.78 | 1.56-1.63 | 0.2269 | 139 | 0.2133 | 2745 | X-RAY DIFFRACTION | 92.02 | 1.63-1.7 | 0.2681 | 175 | 0.2035 | 2776 | X-RAY DIFFRACTION | 92.19 | 1.7-1.79 | 0.222 | 148 | 0.1859 | 2740 | X-RAY DIFFRACTION | 92.18 | 1.79-1.9 | 0.2227 | 157 | 0.179 | 2723 | X-RAY DIFFRACTION | 92.31 | 1.9-2.05 | 0.1998 | 140 | 0.1624 | 2738 | X-RAY DIFFRACTION | 91.95 | 2.05-2.25 | 0.2226 | 134 | 0.158 | 2745 | X-RAY DIFFRACTION | 91.02 | 2.25-2.58 | 0.2026 | 144 | 0.168 | 2706 | X-RAY DIFFRACTION | 91.05 | 2.58-3.24 | 0.1967 | 140 | 0.1683 | 2736 | X-RAY DIFFRACTION | 91.59 | 3.25-19.05 | 0.1522 | 154 | 0.1503 | 2797 | X-RAY DIFFRACTION | 93.56 |
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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 | 2.91517839627 | -1.31464056366 | -0.354630865519 | 3.30972458102 | 1.06483628632 | 7.16842912687 | 0.146869143187 | 0.140062060583 | -0.247006424056 | -0.131260789919 | 0.0296949188141 | -0.00656853558728 | 0.333039049702 | 0.105575523563 | -0.201909291522 | 0.159126152842 | 0.0293078846823 | -0.0202946216296 | 0.0882622694495 | -0.0193696326923 | 0.134893584842 | 15.8287569879 | -7.32103211324 | -27.5012760113 | 2 | 0.564311536239 | 0.0517391236476 | 0.0709176731406 | 1.32495327533 | 0.310930618027 | 0.507308098213 | 0.0322293072783 | -0.0297146738717 | -0.01112741133 | 0.0682997803611 | -0.0354832630891 | 0.0615044803655 | 0.00909570857136 | -0.0116941029135 | 0.00440316756203 | 0.104878350858 | 0.00892905241279 | -0.0187172916311 | 0.114515299503 | -0.00981169739221 | 0.100004592463 | 8.84226342196 | 3.37417968343 | -18.5920236301 | 3 | 0.902581434965 | 0.138631463806 | -0.0972195319733 | 0.957069930363 | -0.596568312941 | 3.30810738012 | -0.0311998952941 | -0.0541614657851 | 0.139799745283 | 0.137572861923 | 0.0231774376484 | 0.0609056162015 | -0.1430266715 | -0.0719245150364 | 0.00450343798298 | 0.173172782034 | 0.0128522841348 | -0.0356419968488 | 0.119394734878 | -0.0356044503304 | 0.159506618282 | 11.9295539862 | 17.1352226442 | -14.3050042212 | 4 | 0.3418942656 | 0.0575266394075 | -0.255790606268 | 0.722899773716 | -0.0384373034574 | 0.903604050578 | 0.0244941792383 | -0.0812088573512 | 0.0076507769527 | 0.0429818088921 | -0.0428737293653 | 0.0512738774325 | -0.0383326949404 | 0.022509169575 | 0.0263908085113 | 0.15939598518 | 0.010802356794 | -0.017641965276 | 0.128648539198 | -0.0232539367573 | 0.144301965118 | 10.9443518308 | 11.4166933582 | -11.3618870938 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A ID | Refine TLS-ID | Selection details | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 0 through 29 )0 - 29 | 1 - 14 | 2 | 2 | chain 'A' and (resid 30 through 145 )30 - 145 | 15 - 130 | 3 | 3 | chain 'A' and (resid 146 through 191 )146 - 191 | 131 - 176 | 4 | 4 | chain 'A' and (resid 192 through 227 )192 - 227 | 177 - 212 | | | | |
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