ソフトウェア | 名称 | バージョン | 分類 |
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xia2 | 0.5.492データ削減 | DIALS | Xia2 0.5.492データ削減 | Aimless | Xia2 0.5.492データスケーリング | Coot | 0.8.9.236モデル構築 | PHASER | v1.13.2998位相決定 | PHENIX | v1.13.2998精密化 | | | | | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.9→51.08 Å / SU ML: 0.2246 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 18.8074 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 | 0.1991 | 1023 | 4.8 % |
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Rwork | 0.1585 | 20311 | - |
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obs | 0.1604 | 21334 | 99.75 % |
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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: 15.51 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→51.08 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2302 | 0 | 0 | 294 | 2596 |
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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_d0.0029 | 2473 | X-RAY DIFFRACTION | f_angle_d0.6068 | 3397 | X-RAY DIFFRACTION | f_chiral_restr0.0429 | 381 | X-RAY DIFFRACTION | f_plane_restr0.0038 | 453 | X-RAY DIFFRACTION | f_dihedral_angle_d11.7214 | 887 | | | | | |
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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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1.9-2 | 0.2827 | 143 | 0.2486 | 2861 | X-RAY DIFFRACTION | 99.6 | 2-2.13 | 0.244 | 164 | 0.2105 | 2852 | X-RAY DIFFRACTION | 99.7 | 2.13-2.29 | 0.2474 | 144 | 0.1905 | 2906 | X-RAY DIFFRACTION | 99.93 | 2.29-2.52 | 0.2314 | 154 | 0.1751 | 2890 | X-RAY DIFFRACTION | 99.74 | 2.52-2.88 | 0.2012 | 141 | 0.1603 | 2900 | X-RAY DIFFRACTION | 99.77 | 2.88-3.63 | 0.1888 | 136 | 0.1294 | 2923 | X-RAY DIFFRACTION | 99.61 | 3.63-51.08 | 0.125 | 141 | 0.1094 | 2979 | X-RAY DIFFRACTION | 99.87 |
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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 | 3.6507480411 | 2.5094421665 | -1.49439114585 | 2.97355391697 | -1.12090645175 | 1.52736216447 | -0.0383585497376 | -0.109955255304 | -0.0150555825427 | -0.0165382713664 | 0.0219307052354 | 0.0169481135598 | 0.0975132048401 | 0.20716647111 | 0.0301917851309 | 0.0863962619568 | 0.0266808672771 | -0.00235432475657 | 0.0929553401693 | -0.0147455993247 | 0.0992468677652 | 16.0483338022 | -12.6176776103 | 26.7013068608 | 2 | 0.364735525899 | -0.0132593998191 | 0.500021897894 | 0.138643740709 | -0.243036996492 | 1.83989948314 | 0.0433109363479 | 0.000974083501655 | 0.0343099693933 | -0.0032495367706 | -0.0176047239325 | -0.0204295392392 | -0.0135797721699 | 0.104542511577 | -0.0162410876553 | 0.112609782742 | -0.00142192629009 | 0.00252671188847 | 0.113269759734 | -0.0036866983258 | 0.120681626249 | 13.861433291 | -7.10237855538 | 9.25011898725 | 3 | 0.526330549832 | -0.208460022673 | -0.215418118833 | 0.8542893813 | -0.728096118107 | 2.11958186733 | 0.0400261049185 | -0.0123918735534 | -0.00344019891182 | -0.094571778511 | -0.0151461782064 | -0.0305763891623 | 0.157907524797 | 0.0933043640754 | -0.0190027602824 | 0.096579797889 | -0.00704297154015 | 0.000343314875604 | 0.100972410805 | -0.0114270409323 | 0.0926861025441 | 7.14452576464 | -13.1753689123 | 2.59555133816 | 4 | 0.394801807805 | -0.264400290075 | -0.502331276754 | 0.77454097559 | 0.334722712191 | 1.38397705442 | -0.000640773964125 | 0.0510909169213 | 0.00980370988745 | -0.0269414755604 | -0.0191699175382 | 0.00470241522063 | -0.0358056814535 | -0.0913048587438 | 0.00252049470447 | 0.1037324205 | -0.00527246379191 | -0.00446503877614 | 0.102656971856 | -0.00822434239624 | 0.0961140980774 | -3.38665009473 | -8.12024105384 | 9.26443499662 | 5 | 0.674148520594 | -1.09280664322 | -1.23888688745 | 4.34840564855 | 2.56243079942 | 2.87463408135 | -0.0101958797401 | 0.120848559418 | -0.0552432155366 | 0.0490517360319 | -0.0750223837663 | 0.206665395688 | 0.125897233638 | -0.150730570833 | 0.138947523008 | 0.0880947066811 | -0.0190258082358 | -0.0364795851013 | 0.149696360835 | -0.00695815693246 | 0.125636164248 | -11.6100002934 | -11.0361985958 | 14.492100809 | 6 | 0.719062331966 | 0.565266119044 | 0.310595525249 | 0.729559631504 | 0.677264992377 | 0.997759454033 | 0.00824764320074 | -0.0328508740721 | 0.0123854245788 | 0.0283826994697 | -0.0159515639604 | 0.0127924598546 | 0.028768260698 | -0.0194091200191 | 0.00952431939145 | 0.0971018570103 | 0.00156266575971 | 0.00687760071704 | 0.0834724678559 | 0.000966401823207 | 0.101155049331 | 0.946333226144 | -8.7360282301 | 25.7259380246 | 7 | 2.75086767571 | 0.365917533839 | -0.799796604588 | 3.24686089146 | -0.164727737389 | 1.47189222938 | 0.116150888258 | 0.0384546050718 | 0.18814244381 | 0.00506107906294 | -0.140871224521 | -0.170333892633 | -0.127676985747 | 0.192701377333 | -0.0510963040791 | 0.0647056545901 | -0.0029175776018 | 0.0104020668046 | 0.14572939228 | -0.0106378510999 | 0.0780206849327 | 13.7045269727 | -1.94622151242 | 32.9026171577 |
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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 1 through 31 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 32 through 100 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 101 through 130 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 131 through 181 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 182 through 196 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 197 through 270 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 271 through 303 ) | | | | | | |
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