ソフトウェア | 名称 | バージョン | 分類 |
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Blu-Ice | | データ収集 | PHASER | | 位相決定 | PHENIX | (phenix.refine: 1.7.2_869)精密化 | XDS | | データ削減 | XDS | | データスケーリング | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRIES 3OZ9 AND 1MEX 解像度: 2.05→46.292 Å / σ(F): 1.34 / 位相誤差: 26.41 / 立体化学のターゲット値: TWIN_LSQ_F
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2091 | 4006 | 5.28 % | GENERATED BY PHENIX.REFINE |
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Rwork | 0.1578 | - | - | - |
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obs | 0.1595 | 75878 | 99.66 % | - |
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all | - | 76062 | - | - |
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溶媒の処理 | 減衰半径: 0.73 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 41.922 Å2 / ksol: 0.372 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.0472 Å2 | -0 Å2 | -0 Å2 |
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2- | - | 2.0472 Å2 | -0 Å2 |
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3- | - | - | -4.0944 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.05→46.292 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6594 | 0 | 52 | 44 | 6690 |
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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 | 6821 | X-RAY DIFFRACTION | f_angle_d1.19 | 9290 | X-RAY DIFFRACTION | f_dihedral_angle_d16.303 | 2427 | X-RAY DIFFRACTION | f_chiral_restr0.071 | 1047 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1171 | | | | | |
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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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2.05-2.0857 | 0.3558 | 202 | 0.294 | 3552 | X-RAY DIFFRACTION | 94 | 2.0857-2.1236 | 0.2832 | 201 | 0.2836 | 3557 | X-RAY DIFFRACTION | 94 | 2.1236-2.1644 | 0.3352 | 201 | 0.279 | 3566 | X-RAY DIFFRACTION | 94 | 2.1644-2.2086 | 0.2787 | 201 | 0.2797 | 3595 | X-RAY DIFFRACTION | 95 | 2.2086-2.2566 | 0.2599 | 192 | 0.2651 | 3561 | X-RAY DIFFRACTION | 95 | 2.2566-2.3091 | 0.2999 | 197 | 0.2595 | 3563 | X-RAY DIFFRACTION | 95 | 2.3091-2.3668 | 0.3207 | 197 | 0.2621 | 3577 | X-RAY DIFFRACTION | 95 | 2.3668-2.4308 | 0.305 | 206 | 0.2588 | 3626 | X-RAY DIFFRACTION | 95 | 2.4308-2.5023 | 0.2987 | 198 | 0.2492 | 3572 | X-RAY DIFFRACTION | 95 | 2.5023-2.583 | 0.2598 | 198 | 0.2366 | 3575 | X-RAY DIFFRACTION | 95 | 2.583-2.6753 | 0.2905 | 198 | 0.2126 | 3627 | X-RAY DIFFRACTION | 95 | 2.6753-2.7824 | 0.2541 | 199 | 0.2048 | 3562 | X-RAY DIFFRACTION | 95 | 2.7824-2.9089 | 0.234 | 201 | 0.1902 | 3590 | X-RAY DIFFRACTION | 95 | 2.9089-3.0622 | 0.2017 | 196 | 0.1752 | 3624 | X-RAY DIFFRACTION | 95 | 3.0622-3.2539 | 0.2545 | 204 | 0.1669 | 3605 | X-RAY DIFFRACTION | 95 | 3.2539-3.5048 | 0.233 | 197 | 0.1511 | 3601 | X-RAY DIFFRACTION | 95 | 3.5048-3.857 | 0.1769 | 203 | 0.1207 | 3606 | X-RAY DIFFRACTION | 94 | 3.857-4.414 | 0.1507 | 201 | 0.0975 | 3598 | X-RAY DIFFRACTION | 94 | 4.414-5.5568 | 0.1345 | 201 | 0.0841 | 3616 | X-RAY DIFFRACTION | 94 | 5.5568-32.7584 | 0.1731 | 206 | 0.1169 | 3660 | X-RAY DIFFRACTION | 92 |
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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 | 0.0262 | -0.0224 | 0.0077 | 0.0678 | -0.0468 | 0.0371 | 0.0738 | 0.0999 | 0.0998 | 0.0328 | -0.0867 | 0.0387 | -0.0087 | 0.1731 | 0.0039 | 0.1153 | -0.1324 | 0.0027 | 0.5033 | 0.0134 | 0.2794 | -15.318 | -11.1144 | 37.1404 | 2 | 0.0395 | 0.0088 | -0.0136 | 0.0038 | -0.0024 | 0.0047 | -0.0166 | -0.0101 | 0.0267 | -0.0602 | 0.0657 | -0.034 | 0.0288 | -0.0494 | 0 | 0.2723 | 0.0899 | -0.0261 | 0.5442 | -0.0278 | 0.2876 | -2.2777 | -17.642 | 2.9191 | 3 | 0.0242 | 0.0426 | 0.0292 | 0.2043 | 0.0393 | 0.0457 | 0.0805 | 0.1332 | 0.0159 | 0.0585 | -0.0048 | -0.005 | 0.0447 | 0.0106 | 0.0278 | 0.0561 | -0.0766 | -0.0155 | 0.5677 | -0.0369 | 0.2438 | -32.9139 | -20.1091 | 25.1652 | 4 | 0.0172 | 0.0004 | -0.0066 | 0.0158 | -0.0205 | 0.0198 | -0.076 | -0.0042 | -0.1087 | -0.0151 | -0.0591 | -0.0737 | 0.1207 | -0.1592 | -0.0009 | 0.1871 | 0.0003 | 0.0192 | 0.4531 | -0.079 | 0.3718 | -6.3843 | -33.1919 | 3.9683 | 5 | 0.1396 | 0.0575 | -0.0455 | 0.0463 | -0.0267 | 0.0263 | 0.0106 | -0.0429 | 0.1291 | -0.0785 | -0.0096 | -0.0325 | 0.1649 | 0.1914 | 0.0196 | 0.317 | 0.1888 | -0.0001 | 0.4492 | 0.0166 | 0.2804 | 35.3585 | -23.4471 | 64.0285 | 6 | 0.0526 | 0.0018 | -0.007 | 0.0198 | 0.0017 | 0.0022 | -0.0199 | -0.0043 | 0.0155 | 0.0943 | 0.0637 | 0.0348 | 0.0611 | -0.0004 | 0.0134 | 0.3372 | 0.1541 | -0.0374 | 0.1832 | 0.017 | 0.2815 | 36.5914 | -38.0689 | 30.3077 | 7 | 0.0265 | 0.0018 | 0.0191 | 0.0014 | 0.0065 | 0.0408 | 0.047 | -0.0276 | 0.0499 | -0.0371 | -0.0349 | 0.0126 | 0.0557 | -0.0481 | 0.0012 | 0.1732 | 0.1148 | 0.0078 | 0.3829 | 0.0307 | 0.2501 | 18.8124 | -12.8376 | 52.3112 | 8 | 0.0079 | -0.0043 | -0.0153 | 0.0128 | -0.0011 | 0.022 | -0.0089 | 0.023 | -0.0701 | 0.0321 | 0.0356 | 0.0912 | 0.0893 | -0.0639 | 0 | 0.3004 | 0.0453 | -0.028 | 0.2658 | 0.0194 | 0.4653 | 20.9967 | -42.1593 | 30.3475 |
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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 H and resid 1:118 or chain H and resid 301:302H1 - 118 | 2 | X-RAY DIFFRACTION | 1 | chain H and resid 1:118 or chain H and resid 301:302H301 - 302 | 3 | X-RAY DIFFRACTION | 2 | chain H and resid 119:213H119 - 213 | 4 | X-RAY DIFFRACTION | 3 | chain L and resid 1:109L1 - 109 | 5 | X-RAY DIFFRACTION | 4 | chain L and resid 110:213L110 - 213 | 6 | X-RAY DIFFRACTION | 5 | chain I and resid 1:118 or chain I and resid 301:301I1 - 118 | 7 | X-RAY DIFFRACTION | 5 | chain I and resid 1:118 or chain I and resid 301:301I301 | 8 | X-RAY DIFFRACTION | 6 | chain I and resid 119:213I119 - 213 | 9 | X-RAY DIFFRACTION | 7 | chain M and resid 1:109M1 - 109 | 10 | X-RAY DIFFRACTION | 8 | chain M and resid 110:213M110 - 213 | | | | | | | | | | | | | | | | | | | | |
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