ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (PHENIX.REFINE)精密化 | MOSFLM | | データ削減 | SCALA | | データスケーリング | CNS | | 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: PDB ENTRY 2BXA 解像度: 2.75→35.124 Å / SU ML: 0.38 / σ(F): 1.98 / 位相誤差: 25.8 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2393 | 1468 | 4.7 % |
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Rwork | 0.2066 | - | - |
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obs | 0.2081 | 30955 | 94.69 % |
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溶媒の処理 | 減衰半径: 0.72 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 38.648 Å2 / ksol: 0.311 e/Å3 |
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原子変位パラメータ | Biso mean: 42.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 43.0395 Å2 | -7.2816 Å2 | 5.4319 Å2 |
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2- | - | 45.6746 Å2 | -3.1258 Å2 |
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3- | - | - | 32.5483 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.75→35.124 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8283 | 0 | 136 | 23 | 8442 |
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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_d0.003 | 8611 | X-RAY DIFFRACTION | f_angle_d0.599 | 11699 | X-RAY DIFFRACTION | f_dihedral_angle_d12.109 | 2992 | X-RAY DIFFRACTION | f_chiral_restr0.043 | 1365 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1529 | | | | | |
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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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2.75-2.8482 | 0.3467 | 131 | 0.288 | 2868 | X-RAY DIFFRACTION | 93 | 2.8482-2.9622 | 0.2847 | 142 | 0.2735 | 2905 | X-RAY DIFFRACTION | 93 | 2.9622-3.097 | 0.3294 | 147 | 0.2752 | 2778 | X-RAY DIFFRACTION | 89 | 3.097-3.2601 | 0.278 | 141 | 0.2419 | 2929 | X-RAY DIFFRACTION | 94 | 3.2601-3.4642 | 0.2624 | 162 | 0.2155 | 2985 | X-RAY DIFFRACTION | 96 | 3.4642-3.7314 | 0.253 | 149 | 0.2103 | 2962 | X-RAY DIFFRACTION | 96 | 3.7314-4.1064 | 0.2311 | 154 | 0.1916 | 2968 | X-RAY DIFFRACTION | 96 | 4.1064-4.6994 | 0.2008 | 148 | 0.1732 | 3028 | X-RAY DIFFRACTION | 97 | 4.6994-5.9162 | 0.2255 | 151 | 0.1952 | 3036 | X-RAY DIFFRACTION | 97 | 5.9162-35.1271 | 0.2175 | 143 | 0.1984 | 3028 | X-RAY DIFFRACTION | 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 | 0.312 | -0.1832 | -0.0609 | 0.4445 | 0.5038 | 0.6639 | -0.0475 | -0.07 | -0.0758 | 0.1484 | -0.0145 | 0.071 | 0.1892 | -0.0548 | -0.3004 | 0.1228 | 0.0025 | 0.1238 | 0.1125 | -0.0101 | -0.0768 | -14.2389 | -2.4416 | 22.6418 | 2 | 0.6402 | 0.0855 | -1.0455 | 0.7718 | -0.3714 | 1.7788 | -0.0051 | -0.0015 | -0.1324 | 0.2958 | -0.1752 | 0.292 | 0.1706 | -0.3718 | 0.0919 | 0.4003 | -0.1002 | 0.1207 | 0.4155 | -0.0875 | 0.3607 | -22.6451 | -2.7874 | 10.8986 | 3 | 0.4288 | -0.3342 | -0.2644 | 0.7665 | -0.3149 | 0.6997 | -0.0119 | 0.0574 | 0.09 | -0.0895 | -0.0863 | 0.0781 | -0.3226 | -0.1044 | -0.0259 | 0.3006 | 0.0845 | -0.03 | 0.123 | -0.0194 | 0.0858 | -6.081 | 14.7395 | 5.8498 | 4 | 0.222 | 0.0601 | -0.0873 | 0.0712 | 0.015 | 0.3032 | 0.0454 | -0.1044 | 0.1123 | 0.0507 | -0.0326 | -0.0356 | -0.0878 | 0.0506 | -1.0745 | 0.0564 | -0.1186 | 0.0969 | 0.0557 | -0.2968 | -0.1389 | 2.3324 | 8.4535 | 14.4373 | 5 | 0.0119 | 0.0029 | -0.001 | 0.0021 | 0.001 | 0.0025 | 0.0121 | -0.0022 | -0.017 | 0.0202 | 0.0082 | -0.0161 | 0.0144 | -0.0005 | 0.0246 | -0.0255 | -0.0633 | -0.044 | -0.0486 | 0.0371 | -0.044 | 2.4004 | -17.7916 | 1.7521 | 6 | 0.0183 | -0.0209 | -0.0043 | 0.1861 | 0.1221 | 0.0837 | 0.0495 | -0.02 | -0.05 | 0.1565 | 0.0355 | -0.0861 | 0.1037 | 0.0131 | 0.9643 | 0.1166 | -0.0314 | -0.133 | 0.0188 | -0.0497 | -0.0073 | 6.9495 | -17.7136 | 6.845 | 7 | 0.0086 | -0.0026 | 0.0002 | 0.0014 | -0.0005 | 0.0009 | -0.0064 | 0.0107 | -0.0142 | -0.0008 | -0.0088 | 0.006 | 0.013 | 0.002 | -0.032 | -0.066 | -0.0844 | -0.0809 | -0.1108 | -0.1151 | -0.0245 | 6.1481 | -23.012 | -11.1546 | 8 | 0.0144 | -0.0118 | 0.0152 | 0.0037 | -0.0084 | 0.0092 | -0.0695 | 0.0228 | -0.0126 | 0.0047 | -0.0062 | -0.0578 | -0.0267 | -0.0192 | -1.0548 | -0.2102 | -0.1972 | -0.1948 | -0.2478 | -0.1332 | -0.2437 | 4.7574 | -1.0999 | -14.9061 | 9 | 0.5183 | 0.0034 | 0.5935 | -0.0011 | 0.0048 | 0.6752 | -0.4106 | -0.3852 | 0.3544 | -0.42 | 0.0334 | 0.1753 | -0.7676 | -0.4347 | 0.5582 | 0.458 | 0.165 | -0.1938 | 0.3149 | -0.1467 | 0.3284 | -2.4559 | 25.7656 | -12.1814 | 10 | 1.6043 | 0.2095 | 1.3342 | 0.6514 | 0.651 | 2.1712 | -0.1683 | -0.0685 | 0.2299 | -0.0666 | -0.0667 | 0.0936 | -0.218 | -0.0885 | 0.1395 | 0.025 | -0.0043 | -0.0551 | -0.0483 | -0.0569 | 0.0386 | 0.5157 | 19.7144 | -14.8472 | 11 | 3.3701 | -0.0141 | 0.635 | 0.8888 | -0.6498 | 2.4831 | -0.1914 | 0.034 | 0.5209 | 0.2902 | -0.1028 | -0.221 | -0.3376 | 0.1115 | 0.2663 | 0.2279 | -0.1336 | -0.152 | 0.1891 | 0.1328 | 0.2124 | 6.6796 | 25.6627 | -19.6817 | 12 | 0.5921 | -0.1895 | 0.3491 | 0.0673 | -0.0986 | 0.23 | -0.112 | -0.2103 | 0.0072 | 0.0496 | 0.0552 | 0.0342 | -0.0714 | -0.1027 | 0.0434 | 1.5511 | -0.1732 | -0.2071 | 2.5442 | 0.8903 | 2.1544 | 0.2704 | 36.2063 | -17.1574 | 13 | 0.4493 | 0.0147 | -0.6804 | 0.2759 | 0.0543 | 1.0517 | 0.0109 | 0.1751 | -0.0048 | -0.0416 | -0.0126 | 0.0741 | -0.0423 | -0.2636 | -0.2277 | 0.0499 | -0.0092 | 0.0326 | 0.1243 | -0.0443 | -0.029 | 44.1474 | 18.273 | 39.2884 | 14 | 0.2403 | -0.0247 | 0.085 | 0.0024 | -0.0015 | 0.4494 | -0.064 | 0.4661 | -0.2318 | -0.0932 | 0.0284 | 0.0435 | 0.0521 | -0.1858 | 0.0494 | 0.2234 | -0.1095 | 0.0731 | 0.6291 | -0.272 | 0.3264 | 44.7196 | 12.1891 | 34.3697 | 15 | 2.7874 | -0.0133 | 1.4886 | 2.3529 | 0.3343 | 0.8445 | 0.2406 | 0.0446 | -0.3022 | -0.7178 | 0.3256 | 0.2472 | 0.216 | -0.685 | -0.5314 | 1.0835 | -0.3981 | -0.1208 | 1.2739 | -0.0043 | 0.4113 | 34.9258 | 16.7769 | 25.984 | 16 | 0.5737 | 0.2026 | 0.1725 | 0.1965 | 0.183 | 0.1917 | -0.2044 | 0.3726 | -0.1069 | -0.1317 | 0.0876 | 0.037 | 0.1181 | -0.1794 | -0.16 | 0.1712 | -0.1353 | 0.0862 | 0.3269 | -0.1139 | 0.1098 | 47.0428 | 13.6658 | 44.0011 | 17 | 0.0261 | -0.0859 | -0.0635 | 0.295 | 0.2861 | 0.6145 | 0.0237 | 0.0125 | 0.0681 | -0.0974 | 0.0691 | -0.1697 | -0.1361 | 0.2138 | -0.1963 | 0.0033 | -0.0808 | 0.2497 | 0.1066 | -0.1731 | -0.0661 | 58.2507 | 27.2095 | 45.9083 | 18 | 0.6527 | -0.0743 | -0.2829 | 0.1352 | 0.1022 | 0.3763 | 0.0513 | 0.261 | 0.1475 | -0.1026 | -0.025 | -0.0031 | -0.0743 | -0.0962 | 0.998 | -0.0843 | -0.0492 | 0.1337 | 0.0858 | 0.1052 | -0.167 | 38.2426 | 36.8514 | 50.6056 | 19 | 0.7507 | -0.0696 | -0.5628 | 0.0225 | 0.041 | 0.4385 | 0.0036 | 0.051 | 0.0171 | -0.0621 | -0.005 | -0.0583 | 0.0007 | -0.0171 | -0.3243 | 0.1452 | -0.0276 | 0.1201 | 0.1332 | 0.0286 | 0.1794 | 30.802 | 49.3003 | 64.7875 | 20 | 0.0032 | -0.0115 | 0.0017 | -0.0027 | -0.0202 | -0.003 | 0.0356 | 0.0046 | 0.1014 | 0.0338 | -0.0274 | 0.0273 | 0.0093 | -0.0243 | 1.9531 | -0.2982 | -0.0752 | 0.2771 | -0.1663 | 0.088 | -0.2084 | 46.2926 | 35.0758 | 73.1215 | 21 | 0.4116 | 0.1208 | 0.2719 | 0.0813 | 0.1562 | 0.3055 | 0.1026 | 0.1041 | -0.1035 | -0.2636 | -0.0688 | -0.2388 | -0.0029 | 0.2678 | 0.1078 | 0.496 | 0.1775 | 0.2649 | 0.4749 | 0.062 | 0.5773 | 71.9382 | 13.2771 | 72.6284 | 22 | 2.9249 | -0.2705 | -2.3006 | 0.6107 | 0.4453 | 2.2712 | -0.0884 | -0.127 | -0.1595 | -0.0096 | -0.0525 | -0.0266 | 0.134 | 0.1391 | 0.0808 | 0.0073 | 0.0533 | 0.0347 | 0.041 | 0.0253 | 0.0385 | 66.8708 | 19.7684 | 74.6396 | 23 | 0.9339 | -0.7289 | -0.8576 | 4.5002 | 0.6376 | 3.4925 | 0.2872 | -0.1841 | -0.0073 | 0.0138 | -0.6393 | -1.2998 | -0.0649 | 0.5905 | 0.2025 | 0.3586 | -0.1849 | -0.0782 | 0.8076 | 0.3399 | 0.6359 | 75.7841 | 22.8288 | 79.3041 | 24 | 0.7778 | 0.5692 | 0.5948 | 1.6892 | 0.2648 | 0.4777 | -0.0542 | -0.837 | -0.0028 | 0.3107 | -0.2409 | -1.0115 | 0.0426 | -0.3594 | 0.2877 | 1.2888 | -0.2126 | -0.3364 | 2.4471 | 1.0003 | 2.2679 | 82.8745 | 12.7386 | 76.0171 |
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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 5:63)2 | X-RAY DIFFRACTION | 2 | (CHAIN A AND RESID 64:106)3 | X-RAY DIFFRACTION | 3 | (CHAIN A AND RESID 107:119)4 | X-RAY DIFFRACTION | 4 | (CHAIN A AND RESID 120:201)5 | X-RAY DIFFRACTION | 5 | (CHAIN A AND RESID 202:240)6 | X-RAY DIFFRACTION | 6 | (CHAIN A AND RESID 241:321)7 | X-RAY DIFFRACTION | 7 | (CHAIN A AND RESID 322:364)8 | X-RAY DIFFRACTION | 8 | (CHAIN A AND RESID 365:497)9 | X-RAY DIFFRACTION | 9 | (CHAIN A AND RESID 498:519)10 | X-RAY DIFFRACTION | 10 | (CHAIN A AND RESID 520:536)11 | X-RAY DIFFRACTION | 11 | (CHAIN A AND RESID 537:560)12 | X-RAY DIFFRACTION | 12 | (CHAIN A AND RESID 561:582)13 | X-RAY DIFFRACTION | 13 | (CHAIN B AND RESID 5:38)14 | X-RAY DIFFRACTION | 14 | (CHAIN B AND RESID 39:50)15 | X-RAY DIFFRACTION | 15 | (CHAIN B AND RESID 51:56)16 | X-RAY DIFFRACTION | 16 | (CHAIN B AND RESID 57:133)17 | X-RAY DIFFRACTION | 17 | (CHAIN B AND RESID 134:196)18 | X-RAY DIFFRACTION | 18 | (CHAIN B AND | | | | | | | | | | | | | | | | | |
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