ソフトウェア | 名称 | バージョン | 分類 |
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ADSC | Quantumデータ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.6.4_486)精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHENIX | | 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: 1F3H 解像度: 2.4→31.072 Å / SU ML: 0.44 / σ(F): 1.34 / σ(I): 0 / 位相誤差: 34.79 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2501 | 1021 | 5.09 % | RANDOM |
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Rwork | 0.2132 | - | - | - |
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obs | 0.2151 | 20063 | 97.94 % | - |
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all | - | 20484 | - | - |
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溶媒の処理 | 減衰半径: 0.95 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 73.478 Å2 / ksol: 0.331 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- | 9.852 Å2 | 0 Å2 | 18.7977 Å2 |
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2- | - | -15.705 Å2 | 0 Å2 |
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3- | - | - | 5.853 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.4→31.072 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2305 | 0 | 2 | 22 | 2329 |
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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_d0.01 | 2361 | X-RAY DIFFRACTION | f_angle_d1.224 | 3173 | X-RAY DIFFRACTION | f_dihedral_angle_d19.449 | 911 | X-RAY DIFFRACTION | f_chiral_restr0.079 | 323 | X-RAY DIFFRACTION | f_plane_restr0.007 | 415 | | | | | |
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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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2.4-2.5265 | 0.4878 | 135 | 0.4052 | 2482 | X-RAY DIFFRACTION | 90 | 2.5265-2.6847 | 0.3841 | 120 | 0.3499 | 2734 | X-RAY DIFFRACTION | 99 | 2.6847-2.8918 | 0.3241 | 135 | 0.2669 | 2765 | X-RAY DIFFRACTION | 100 | 2.8918-3.1826 | 0.3165 | 141 | 0.2614 | 2770 | X-RAY DIFFRACTION | 100 | 3.1826-3.6425 | 0.3072 | 179 | 0.2438 | 2743 | X-RAY DIFFRACTION | 100 | 3.6425-4.5868 | 0.2055 | 147 | 0.176 | 2802 | X-RAY DIFFRACTION | 100 | 4.5868-31.0743 | 0.2071 | 164 | 0.1828 | 2746 | X-RAY DIFFRACTION | 98 |
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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 | 0.5611 | -0.0916 | -0.2445 | 1.2799 | -0.2574 | 0.4049 | -0.0181 | 0.1953 | 1.8499 | -0.5827 | 0.7239 | -3.0632 | 1.085 | 0.4427 | -0.1227 | 0.5723 | 0.0451 | -0.0059 | 0.8356 | -0.1591 | 0.664 | 16.3129 | 4.2809 | 14.9251 | 2 | 0.4193 | 0.0288 | -0.1406 | 0.4959 | -0.3615 | 0.3195 | 0.0242 | -0.446 | -0.2483 | 0.9137 | 0.0443 | 1.0991 | 0.1337 | 0.1453 | -0.086 | 0.6528 | 0.0097 | 0.0419 | 0.6177 | -0.0784 | 0.6163 | 21.0606 | -6.3805 | 12.7658 | 3 | 0.6356 | 0.3203 | -1.2458 | 0.4456 | -0.3512 | 0.7756 | -0.4005 | -0.4266 | -0.428 | 0.271 | 0.3714 | -0.0063 | 0.6628 | 0.0772 | -0.0733 | 0.7671 | 0.0568 | 0.0066 | 0.5944 | -0.0773 | 0.5732 | 27.0173 | -15.3444 | 10.4177 | 4 | 2.3338 | 0.1995 | -0.6923 | 0.9424 | -1.0897 | 1.073 | -0.2869 | 0.6797 | -0.3245 | -1.2037 | 0.4702 | -0.3284 | -0.1799 | 0.5258 | -0.068 | 0.9027 | 0.0609 | -0.0356 | 0.6488 | -0.1074 | 0.5528 | 25.7905 | -6.6688 | 0.8891 | 5 | 2.207 | 0.3539 | -0.9147 | 0.9246 | -1.3957 | 1.5535 | -0.0029 | 0.432 | -0.5674 | -0.516 | 0.3798 | -1.1812 | 0.4616 | 0.4819 | -0.061 | 0.6052 | 0.1483 | -0.0096 | 0.5576 | -0.1528 | 0.6335 | 35.9293 | -8.4251 | 7.7206 | 6 | 3.793 | -1.855 | -0.404 | 0.8829 | 0.4438 | 1.2871 | -0.1628 | 0.0169 | 0.4062 | -0.652 | 0.3219 | -0.5721 | 0.5143 | -0.07 | -0.1209 | 0.5697 | 0.0553 | -0.0005 | 0.4055 | -0.124 | 0.5873 | 28.9061 | 6.7465 | 14.4084 | 7 | 0.9611 | 0.4915 | -0.2565 | 0.3406 | 0.2225 | 1.1961 | -0.2454 | -0.4126 | -0.0351 | -0.2828 | 0.7099 | -0.8737 | -0.0334 | -1.2728 | -0.1564 | 0.956 | -0.0342 | 0.0711 | 0.6915 | 0.016 | 0.772 | 29.4908 | 6.1288 | -8.0633 | 8 | 1.5072 | -0.6595 | -0.4998 | 0.1115 | 0.1347 | 1.3959 | 0.1622 | 0.2221 | -0.3673 | 0.598 | 0.1602 | -0.5381 | 0.1774 | 1.0816 | -0.1052 | 0.5576 | -0.0141 | 0.0318 | 0.6685 | 0.0448 | 0.5831 | 30.7217 | 3.2146 | -25.4116 | 9 | 0.5568 | 0.1737 | -0.1061 | 0.2055 | 0.1256 | 0.2792 | 0.0013 | 0.2666 | 0.5123 | 0.7612 | -0.3582 | -1.715 | 1.3319 | -0.7251 | -0.1455 | 0.9147 | 0.109 | 0.09 | 0.9436 | -0.0392 | 0.6186 | 15.366 | 14.1812 | 16.9979 | 10 | 0.473 | 0.2575 | 0.5385 | 0.2972 | -0.0662 | 0.3661 | 0.0873 | 0.4093 | -0.0091 | -1.9478 | -0.1789 | -0.7454 | 0.4788 | 0.65 | -0.1672 | 0.7232 | 0.0512 | 0.0337 | 0.6273 | 0.0317 | 0.7325 | 14.1347 | 25.2145 | 22.7636 | 11 | 0.505 | 0.1899 | 0.3277 | 0.5615 | -0.1396 | 0.6721 | -1.892 | -0.8291 | 3.1912 | 0.7889 | 1.3642 | 0.6267 | -1.0309 | 0.7667 | -0.1765 | 0.9023 | -0.0068 | 0.0086 | 0.5496 | -0.1544 | 1.9569 | 14.4416 | 33.8364 | 30.4106 | 12 | 0.7034 | 0.9028 | 1.1034 | 1.0878 | 0.8051 | 1.363 | -0.0408 | -0.3261 | 0.1971 | 0.7036 | -0.6038 | 2.2008 | -0.4096 | -0.3138 | -0.1685 | 0.4809 | 0.0965 | 0.044 | 0.6553 | -0.3298 | 1.3104 | 4.8071 | 25.9909 | 29.8801 | 13 | 1.2783 | 0.5242 | 0.9573 | 0.1398 | 0.4775 | 0.5527 | -0.2881 | -1.3993 | 1.7231 | 1.6381 | 1.0567 | 0.2374 | -0.1705 | -0.0089 | -0.1623 | 0.9994 | -0.0845 | 0.2844 | 0.7747 | -0.2814 | 0.9888 | 12.6112 | 23.7559 | 38.8572 | 14 | 0.7935 | 0.1725 | -0.2582 | 0.1304 | 0.089 | 0.2571 | -0.5978 | -0.7951 | 2.3218 | 0.7263 | 1.0475 | -0.6756 | -0.6452 | 0.8099 | -0.1232 | 0.9245 | 0.0858 | -0.2129 | 0.9261 | -0.3875 | 0.8999 | 25.4085 | 15.9103 | 28.961 | 15 | 0.7759 | -0.1998 | -0.3431 | 1.1731 | 1.6078 | 1.1443 | -0.4779 | -0.3675 | -0.515 | 1.1082 | 0.2606 | 0.6239 | 0.8789 | -0.0294 | -0.1238 | 0.8131 | -0.0297 | 0.1039 | 0.614 | -0.0906 | 0.9289 | 11.0116 | 8.7309 | 29.4701 | 16 | 1.5257 | 0.3175 | 0.0259 | 0.5899 | 0.207 | 1.7364 | 0.0325 | -1.3725 | 1.1672 | -0.288 | 0.1631 | -1.0681 | -0.3609 | 0.4225 | -0.169 | 0.8721 | -0.1131 | 0.2406 | 0.6296 | -0.0657 | 0.7613 | -20.8171 | 12.6364 | 36.2018 |
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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 5:11)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 12:23)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 24:43)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 44:65)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 66:89)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 90:115)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 116:122)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 123:139)9 | X-RAY DIFFRACTION | 9 | (chain B and resid 5:11)10 | X-RAY DIFFRACTION | 10 | (chain B and resid 12:24)11 | X-RAY DIFFRACTION | 11 | (chain B and resid 25:40)12 | X-RAY DIFFRACTION | 12 | (chain B and resid 41:68)13 | X-RAY DIFFRACTION | 13 | (chain B and resid 69:89)14 | X-RAY DIFFRACTION | 14 | (chain B and resid 90:95)15 | X-RAY DIFFRACTION | 15 | (chain B and resid 96:118)16 | X-RAY DIFFRACTION | 16 | (chain B and resid 119:140) | | | | | | | | | | | | | | | |
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