ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0019精密化 | ADSC | Quantumデータ収集 | XDS | | データ削減 | XSCALE | | データスケーリング | REFMAC | | 位相決定 | | |
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精密化 | 構造決定の手法: フーリエ合成 / 解像度: 1.9→47.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.42 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.108 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.18124 | 504 | 1 % | RANDOM |
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Rwork | 0.14864 | - | - | - |
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all | 0.14897 | 50735 | - | - |
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obs | 0.14897 | 50735 | 99.96 % | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 11.174 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.31 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.31 Å2 | 0 Å2 |
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3- | - | - | 0.63 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→47.4 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4524 | 0 | 65 | 354 | 4943 |
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拘束条件 | Refine-ID | タイプ | Dev ideal |
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X-RAY DIFFRACTION | r_bond_refined_d0.022 | X-RAY DIFFRACTION | r_bond_other_d0.002 | X-RAY DIFFRACTION | r_angle_refined_deg1.911 | X-RAY DIFFRACTION | r_angle_other_deg0.983 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.605 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.413 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.717 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.58 | X-RAY DIFFRACTION | r_chiral_restr | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.9→2.003 Å / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.205 | 67 | - |
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Rwork | 0.152 | 7301 | - |
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obs | - | - | 99.97 % |
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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 | 1.4791 | 0.2965 | -0.2289 | 1.6695 | -0.0869 | 1.4465 | -0.0003 | 0.1253 | 0.0026 | -0.0668 | 0.0124 | 0.0305 | -0.0172 | -0.07 | -0.0121 | 0.0573 | -0.0046 | 0.0023 | 0.0795 | -0.0076 | 0.0448 | 68.6426 | 51.0744 | 17.207 | 2 | 1.051 | 0.0768 | -0.0251 | 0.2395 | -0.6836 | 1.988 | 0.0175 | -0.1802 | 0.1256 | 0.1265 | -0.0155 | 0.2079 | -0.1923 | -0.2701 | -0.002 | 0.0442 | -0.0116 | 0.0034 | 0.0815 | -0.0097 | 0.0696 | 52.1675 | 59.9679 | 33.0099 | 3 | 1.016 | 0.4805 | -0.339 | 0.5136 | -0.2274 | 0.1288 | 0.0148 | -0.0443 | -0.0237 | 0.0011 | -0.0038 | -0.0312 | -0.036 | 0.0031 | -0.011 | 0.0574 | -0.0041 | 0.0054 | 0.0734 | -0.0093 | 0.0451 | 60.421 | 35.2746 | 51.4149 | 4 | 0.5198 | -0.5665 | 1.1635 | 1.2379 | -2.0655 | 4.5449 | -0.0279 | -0.0433 | 0.0198 | 0.1037 | -0.0234 | -0.0622 | -0.0367 | 0.1029 | 0.0513 | 0.0716 | 0.0035 | 0.0184 | 0.0833 | -0.0136 | 0.06 | 68.2333 | 47.3385 | 40.038 | 5 | 1.8582 | 0.3269 | -0.2986 | 0.9821 | -0.1888 | 1.4882 | 0.001 | 0.0343 | 0.0612 | -0.0268 | -0.0185 | -0.1847 | -0.1085 | 0.2707 | 0.0175 | 0.0837 | -0.0101 | 0.0147 | 0.0745 | -0.0052 | 0.0726 | 80.1348 | 66.6011 | 29.0851 | 6 | 0.7664 | -0.1725 | -0.6719 | 1.666 | 1.8233 | 2.4732 | 0.0739 | 0.1283 | 0.0643 | -0.1568 | -0.0633 | 0.0075 | -0.1582 | -0.1572 | -0.0106 | 0.0718 | 0.0112 | 0.0011 | 0.0609 | 0.0204 | 0.0565 | 62.2251 | 77.9202 | 37.1073 | 7 | 12.0005 | 5.4137 | 3.4572 | 2.7771 | -0.0054 | 8.3113 | -0.1201 | -0.2527 | 0.668 | 0.3419 | -0.064 | 0.0705 | -0.401 | -0.197 | 0.1842 | 0.0986 | -0.0027 | 0.0006 | 0.0566 | 0.0079 | 0.0778 | 72.7551 | 83.594 | 49.6051 | 8 | 0.3775 | -0.0125 | 0.0396 | 1.1049 | 0.8033 | 0.957 | -0.0115 | 0.0838 | -0.002 | -0.1251 | -0.0605 | 0.1528 | -0.096 | -0.0988 | 0.072 | 0.0787 | -0.0021 | 0.003 | 0.0897 | 0.0194 | 0.0685 | 62.0743 | 67.2644 | 27.0001 | 9 | 2.4944 | 0.705 | -0.9284 | 2.5259 | -0.8354 | 4.0775 | 0.0273 | 0.368 | 0.0738 | -0.2293 | 0.0708 | 0.2086 | -0.1859 | -0.2136 | -0.0981 | 0.0836 | -0.0124 | 0.0102 | 0.1406 | -0.0432 | 0.0755 | 65.9335 | 48.3964 | 12.3216 | 10 | 7.4637 | -0.3053 | -1.2236 | 1.0832 | 0.098 | 1.1376 | -0.0234 | 0.225 | -0.2705 | -0.0628 | -0.0014 | 0.0484 | 0.0818 | -0.085 | 0.0248 | 0.0783 | -0.0078 | 0.0181 | 0.0533 | -0.0292 | 0.0705 | 76.4138 | 36.2008 | 19.383 | 11 | 2.0311 | -0.2009 | -0.766 | 2.123 | 0.0226 | 2.5558 | -0.0619 | -0.1641 | -0.2213 | 0.1676 | 0.0307 | -0.1189 | 0.2303 | 0.2076 | 0.0312 | 0.0587 | -0.0005 | 0.0239 | 0.0677 | -0.0176 | 0.115 | 79.1219 | 39.4438 | 28.3747 | 12 | 3.6659 | 0.1758 | -1.3003 | 4.6697 | 3.1879 | 5.9845 | -0.0853 | 0.0516 | -0.2632 | -0.0015 | 0.0593 | -0.1705 | 0.1103 | 0.1834 | 0.0259 | 0.0718 | -0.0025 | -0.0025 | 0.0852 | 0.0226 | 0.0885 | 85.1653 | 45.7943 | 36.5933 | 13 | 1.4262 | -0.995 | 0.2198 | 2.4167 | -0.1478 | 0.6703 | -0.0596 | -0.0134 | 0.1581 | 0.0997 | 0.0243 | 0.0492 | -0.1229 | -0.0868 | 0.0352 | 0.0687 | -0.0055 | -0.0002 | 0.0883 | -0.0036 | 0.0641 | 55.5221 | 80.0683 | 50.5676 | 14 | 5.3598 | -0.8771 | -0.5764 | 1.9441 | 0.4475 | 1.2706 | -0.0421 | 0.0142 | 0.201 | -0.0796 | 0.0215 | 0.0739 | -0.0532 | -0.0565 | 0.0206 | 0.0784 | 0.008 | -0.0346 | 0.051 | 0.0459 | 0.0857 | 48.1557 | 92.4694 | 43.1076 | 15 | 2.0816 | -0.9788 | -0.1872 | 0.8386 | 0.0967 | 0.5034 | -0.0117 | 0.1147 | -0.0419 | -0.0321 | -0.0202 | 0.1158 | -0.0306 | -0.0747 | 0.0319 | 0.082 | -0.0112 | 0.001 | 0.0697 | 0.0098 | 0.0686 | 58.1539 | 75.6334 | 43.267 | 16 | 3.623 | -1.1147 | -1.0943 | 2.5103 | 0.2532 | 0.3338 | -0.1116 | 0.0728 | -0.4584 | -0.0512 | 0.0232 | -0.014 | 0.4811 | 0.0829 | 0.0884 | 0.0962 | -0.0132 | -0.0012 | 0.0546 | -0.0059 | 0.036 | 50.061 | 65.6626 | 49.6014 | 17 | 1.5586 | -1.5204 | -0.9145 | 2.0785 | 0.8796 | 0.6066 | -0.0696 | -0.0469 | -0.1005 | 0.0389 | 0.0987 | -0.0634 | 0.0646 | 0.0968 | -0.0291 | 0.0696 | -0.0021 | 0.0027 | 0.0779 | 0.0005 | 0.0564 | 73.3543 | 61.2544 | 46.3988 | 18 | 3.8737 | 1.071 | 0.9855 | 3.1169 | 0.1234 | 2.4048 | 0.0657 | -0.0168 | -0.2466 | 0.0443 | -0.0173 | -0.0405 | 0.2725 | -0.0254 | -0.0484 | 0.0818 | 0.0006 | 0.0343 | 0.0802 | 0.0064 | 0.0929 | 74.076 | 38.0781 | 39.9801 | 19 | 1.4365 | -0.5779 | -0.1734 | 1.1174 | 0.033 | 0.7327 | -0.0358 | 0.089 | -0.116 | -0.0419 | 0.0119 | -0.0585 | 0.0988 | 0.0519 | 0.0238 | 0.0716 | -0.0028 | 0.0012 | 0.0812 | 0.0024 | 0.0483 | 70.2382 | 63.5427 | 52.3573 | 20 | 0.9115 | -0.2555 | -0.2761 | 0.9599 | 0.2887 | 1.5127 | -0.0273 | 0.0585 | -0.0272 | -0.0312 | 0.0242 | -0.1008 | 0.0219 | 0.0687 | 0.0031 | 0.0581 | -0.0185 | 0.0235 | 0.0723 | -0.0107 | 0.0912 | 83.4097 | 53.9269 | 25.0291 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA46 - 85 | 46 - 85 | 2 | X-RAY DIFFRACTION | 2 | AA86 - 107 | 86 - 107 | 3 | X-RAY DIFFRACTION | 3 | AA108 - 146 | 108 - 146 | 4 | X-RAY DIFFRACTION | 4 | AA147 - 165 | 147 - 165 | 5 | X-RAY DIFFRACTION | 5 | AA166 - 205 | 166 - 205 | 6 | X-RAY DIFFRACTION | 6 | AA206 - 227 | 206 - 227 | 7 | X-RAY DIFFRACTION | 7 | AA228 - 233 | 228 - 233 | 8 | X-RAY DIFFRACTION | 8 | AA234 - 265 | 234 - 265 | 9 | X-RAY DIFFRACTION | 9 | AA266 - 285 | 266 - 285 | 10 | X-RAY DIFFRACTION | 10 | AA286 - 307 | 286 - 307 | 11 | X-RAY DIFFRACTION | 11 | AA308 - 346 | 308 - 346 | 12 | X-RAY DIFFRACTION | 12 | AA347 - 358 | 347 - 358 | 13 | X-RAY DIFFRACTION | 13 | AA359 - 385 | 359 - 385 | 14 | X-RAY DIFFRACTION | 14 | AA386 - 413 | 386 - 413 | 15 | X-RAY DIFFRACTION | 15 | AA414 - 452 | 414 - 452 | 16 | X-RAY DIFFRACTION | 16 | AA453 - 466 | 453 - 466 | 17 | X-RAY DIFFRACTION | 17 | AA467 - 483 | 467 - 483 | 18 | X-RAY DIFFRACTION | 18 | AA484 - 505 | 484 - 505 | 19 | X-RAY DIFFRACTION | 19 | AA506 - 548 | 506 - 548 | 20 | X-RAY DIFFRACTION | 20 | AA549 - 618 | 549 - 618 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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