ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.3.0037精密化 | MAR345 | | データ収集 | DENZO | | データ削減 | SCALEPACK | | 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 開始モデル: PDB ENTRY 1R5D 解像度: 1.6→27.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.101 / 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 | 0.22638 | 1605 | 5 % | RANDOM |
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Rwork | 0.18414 | - | - | - |
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obs | 0.18628 | 30202 | 99.83 % | - |
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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: MASK |
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Refine analyze | Luzzati coordinate error obs: 0.206 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→27.7 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1882 | 0 | 50 | 327 | 2259 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.008 | 0.022 | 1978 | X-RAY DIFFRACTION | r_angle_refined_deg1.171 | 1.978 | 2667 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.517 | 5 | 246 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.296 | 24.865 | 74 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.936 | 15 | 365 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.447 | 15 | 8 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 1428 | X-RAY DIFFRACTION | r_nbd_refined0.192 | 0.2 | 991 | X-RAY DIFFRACTION | r_nbtor_refined0.291 | 0.2 | 1359 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.121 | 0.2 | 263 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.168 | 0.2 | 53 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.137 | 0.2 | 44 | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.6→1.641 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.282 | 114 | - |
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Rwork | 0.229 | 2161 | - |
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obs | - | - | 98.4 % |
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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 | 6.7081 | -0.1307 | -1.113 | 3.1265 | 2.6762 | 12.7358 | 0.0871 | -0.4358 | 0.123 | 0.3413 | -0.0743 | -0.1358 | 0.0615 | 0.4535 | -0.0128 | 0.0442 | -0.025 | -0.004 | 0.0404 | -0.0002 | -0.002 | 10.348 | 19.9404 | 24.6128 | 2 | 1.6362 | -0.1106 | 0.9097 | 3.827 | -3.1014 | 5.6051 | 0.0281 | 0.0096 | 0.1013 | -0.1964 | -0.125 | -0.108 | 0.0334 | 0.1881 | 0.0969 | 0.0264 | -0.0042 | 0.0072 | 0.0393 | 0.0043 | 0.0285 | 9.8336 | 20.6782 | 14.7305 | 3 | 6.4465 | -1.0189 | 4.0615 | 2.3833 | -3.7912 | 7.0218 | 0.5459 | 0.5591 | -0.0831 | 0.0375 | 0.0843 | 0.2922 | 0.5105 | -0.7 | -0.6302 | 0.0255 | 0.0141 | -0.003 | 0.1039 | 0.017 | 0.0746 | 10.6988 | 25.9045 | 1.047 | 4 | 1.3869 | 0.7599 | 0.2989 | 2.4264 | -1.3905 | 3.5607 | 0.0269 | -0.0975 | -0.05 | -0.0194 | -0.055 | 0.1971 | -0.0108 | -0.0335 | 0.0281 | -0.0053 | -0.0013 | 0.002 | 0.0243 | 0.0035 | 0.0521 | 21.0128 | 27.8356 | 7.247 | 5 | 12.1027 | -4.6938 | -2.2313 | 3.5229 | 2.8161 | 2.6464 | 0.0086 | -1.0577 | 0.0361 | 0.5882 | 0.1084 | -0.159 | -0.1552 | -0.049 | -0.117 | 0.0738 | -0.0251 | 0.0103 | 0.1418 | 0.0224 | -0.0305 | 23.6133 | 32.1734 | 16.6379 | 6 | 3.1847 | 0.0864 | -0.6928 | 0.7019 | -0.135 | 1.0201 | 0.1296 | 0.0352 | -0.1794 | 0.0138 | -0.0935 | -0.0178 | -0.0382 | 0.0048 | -0.0361 | 0.032 | 0.0104 | -0.0161 | 0.0149 | -0.0081 | 0.0522 | 34.2464 | 31.4354 | 1.8107 | 7 | 2.1124 | -2.5756 | -1.8022 | 7.417 | 5.0652 | 6.498 | 0.1566 | 0.0324 | -0.0082 | -0.261 | -0.0167 | -0.1188 | -0.417 | -0.0411 | -0.1399 | 0.0466 | -0.0186 | 0.0169 | -0.0025 | 0.0014 | 0.0052 | 42.2868 | 43.8107 | 2.6759 | 8 | 3.584 | 0.7452 | -0.0411 | 1.43 | 0.2012 | 0.9017 | 0.113 | 0.2361 | -0.0232 | -0.039 | -0.0453 | -0.0204 | -0.0428 | 0.0257 | -0.0677 | 0.0564 | 0.0171 | -0.0089 | 0.0241 | 0.0134 | 0.0311 | 33.9524 | 36.831 | -1.0823 | 9 | 6.6546 | 2.5084 | -3.6268 | 7.9976 | -13.524 | 22.9337 | 0.1146 | -0.4838 | 0.2698 | 0.5619 | 0.3808 | 0.8226 | -0.9657 | -0.8758 | -0.4954 | 0.0213 | 0.0707 | 0.0867 | 0.049 | -0.0366 | 0.0373 | 13.6733 | 37.8512 | 14.2641 | 10 | 5.4566 | 0.8431 | -3.1312 | 1.1193 | -0.5601 | 5.268 | -0.0481 | 0.2605 | 0.0831 | -0.0642 | 0.0743 | 0.1432 | 0.173 | -0.2133 | -0.0262 | 0.0547 | 0.0211 | -0.0195 | 0.0065 | 0.0109 | 0.0565 | 23.297 | 35.6201 | -1.0898 | 11 | 3.8082 | -2.2473 | 3.5218 | 3.3248 | -2.6047 | 6.4102 | -0.1164 | 0.2066 | 0.0346 | 0.0876 | 0.0163 | -0.2189 | -0.1149 | 0.2151 | 0.1 | 0.0396 | -0.0072 | -0.0129 | 0.039 | 0.0047 | 0.0545 | 42.8312 | 35.3473 | 4.8154 | 12 | 6.2026 | -4.3508 | 3.2041 | 4.5756 | -2.4878 | 3.1768 | 0.0548 | -0.0995 | 0.0239 | -0.1262 | 0.0281 | -0.0115 | -0.0469 | -0.1055 | -0.083 | 0.0381 | -0.0172 | -0.0141 | 0.0099 | 0.0106 | 0.0265 | 38.6133 | 36.225 | 4.3311 | 13 | 6.3801 | 0.7649 | 1.5499 | 2.1408 | 0.3186 | 1.9327 | 0.0368 | -0.3953 | -0.0731 | 0.2027 | -0.1223 | -0.0979 | -0.0354 | 0.0075 | 0.0854 | 0.0145 | -0.0253 | -0.0156 | 0.0354 | 0.0217 | 0.0305 | 34.9026 | 28.7803 | 10.54 | 14 | 6.4256 | 1.9764 | -1.4644 | 7.8552 | 3.841 | 2.8749 | -0.4637 | 0.9345 | -0.0196 | -0.1616 | 0.2135 | 0.4426 | -0.0231 | -0.3814 | 0.2502 | 0.0011 | -0.0421 | 0.0158 | 0.0368 | 0.0371 | 0.0342 | 22.3415 | 22.1654 | -2.0687 | 15 | 4.8011 | 2.6771 | -0.8305 | 1.7636 | -0.8495 | 8.1189 | -0.105 | -0.0747 | 0.1192 | -0.2584 | 0.0694 | -0.1569 | 0.0845 | 0.1961 | 0.0356 | 0.0307 | 0.0055 | 0.0499 | -0.0108 | 0.0191 | 0.05 | 18.3665 | 19.0057 | 7.147 | 16 | 3.594 | 1.1696 | -2.0424 | 6.8093 | -0.9693 | 1.609 | 0.1571 | -0.2697 | -0.0826 | 0.2437 | -0.1659 | -0.1659 | -0.0477 | 0.238 | 0.0088 | 0.0064 | -0.0083 | -0.0051 | 0.0588 | 0.03 | 0.0226 | 18.7622 | 20.6713 | 15.6227 | 17 | 17.2157 | 5.0733 | -4.3993 | 9.5687 | -0.9877 | 7.4391 | 0.2716 | -1.7705 | -0.3405 | 0.5527 | -0.3088 | -0.9443 | -0.0425 | 1.0318 | 0.0372 | -0.0558 | 0.0186 | -0.0144 | 0.1721 | 0.0667 | 0.0812 | 22.9504 | 12.9144 | 17.2418 | 18 | 2.0186 | 0.0287 | -0.1512 | 2.1066 | -0.9552 | 1.6667 | -0.0193 | -0.0293 | -0.0259 | -0.0191 | 0.0576 | 0.0964 | 0.0395 | -0.1799 | -0.0383 | 0.0313 | 0.0043 | -0.0081 | 0.0413 | 0.0055 | 0.0113 | 2.0345 | 17.0256 | 14.5976 | 19 | 12.9111 | -8.035 | 8.8923 | 9.7058 | -5.839 | 6.1441 | 0.2493 | -0.1148 | -0.2954 | -0.2593 | 0.2701 | 0.4503 | 0.3546 | -0.1365 | -0.5194 | 0.0295 | -0.0186 | -0.0072 | 0.0868 | 0.046 | -0.0024 | 0.3884 | 3.2755 | 21.0796 | 20 | 0.9387 | -0.6571 | 1.8651 | 7.8534 | -7.8037 | 13.1519 | 0.0084 | 0.0497 | -0.0708 | -0.0252 | 0.325 | 0.371 | 0.0287 | -0.3902 | -0.3335 | -0.0079 | -0.0181 | -0.0008 | 0.0594 | 0.023 | 0 | -3.005 | 9.3785 | 19.224 | 21 | 8.6698 | -0.2343 | -0.456 | 3.1432 | 0.679 | 2.294 | -0.2547 | 0.1278 | 0.1297 | -0.2004 | 0.2388 | 0.027 | 0.3582 | -0.1464 | 0.0159 | 0.096 | -0.0224 | -0.0119 | 0.0237 | 0.0046 | -0.0073 | 4.0024 | 15.4325 | 6.6348 | 22 | 1.7351 | 0.6636 | 2.1434 | 3.38 | -0.2824 | 7.01 | 0.0823 | 0.1544 | -0.2879 | -0.2072 | -0.1738 | -0.8514 | 0.2532 | 1.0235 | 0.0915 | -0.0189 | 0.0735 | 0.082 | 0.0526 | 0.0751 | 0.1456 | 24.7864 | 9.5087 | 9.3399 | 23 | 8.0739 | 0.0789 | -0.7375 | 0.2263 | -0.6972 | 2.1783 | -0.1574 | 0.4669 | -0.0678 | -0.2519 | 0.072 | -0.0932 | 0.3496 | -0.1435 | 0.0855 | 0.1131 | -0.012 | 0.036 | -0.0296 | -0.0092 | 0.0197 | 7.9182 | 12.1489 | 5.2143 | 24 | 1.047 | -0.9189 | -1.7909 | 7.4468 | 5.9806 | 10.5239 | 0.0423 | -0.0554 | -0.0335 | 0.02 | 0.0548 | -0.06 | 0.1525 | -0.2208 | -0.0971 | 0.0323 | -0.01 | -0.0011 | 0.0458 | 0.0078 | 0.0044 | 2.1668 | 12.9527 | 21.0459 |
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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 | AA1 - 9 | 1 - 9 | 2 | X-RAY DIFFRACTION | 2 | AA10 - 16 | 10 - 16 | 3 | X-RAY DIFFRACTION | 3 | AA17 - 23 | 17 - 23 | 4 | X-RAY DIFFRACTION | 4 | AA24 - 33 | 24 - 33 | 5 | X-RAY DIFFRACTION | 5 | AA34 - 39 | 34 - 39 | 6 | X-RAY DIFFRACTION | 6 | AA40 - 59 | 40 - 59 | 7 | X-RAY DIFFRACTION | 7 | AA60 - 69 | 60 - 69 | 8 | X-RAY DIFFRACTION | 8 | AA70 - 86 | 70 - 86 | 9 | X-RAY DIFFRACTION | 9 | AA87 - 94 | 87 - 94 | 10 | X-RAY DIFFRACTION | 10 | AA95 - 105 | 95 - 105 | 11 | X-RAY DIFFRACTION | 11 | AA106 - 113 | 106 - 113 | 12 | X-RAY DIFFRACTION | 12 | AA114 - 124 | 114 - 124 | 13 | X-RAY DIFFRACTION | 13 | BB1 - 14 | 1 - 14 | 14 | X-RAY DIFFRACTION | 14 | BB15 - 23 | 15 - 23 | 15 | X-RAY DIFFRACTION | 15 | BB24 - 30 | 24 - 30 | 16 | X-RAY DIFFRACTION | 16 | BB31 - 35 | 31 - 35 | 17 | X-RAY DIFFRACTION | 17 | BB36 - 41 | 36 - 41 | 18 | X-RAY DIFFRACTION | 18 | BB42 - 61 | 42 - 61 | 19 | X-RAY DIFFRACTION | 19 | BB62 - 68 | 62 - 68 | 20 | X-RAY DIFFRACTION | 20 | BB69 - 77 | 69 - 77 | 21 | X-RAY DIFFRACTION | 21 | BB78 - 83 | 78 - 83 | 22 | X-RAY DIFFRACTION | 22 | BB84 - 96 | 84 - 96 | 23 | X-RAY DIFFRACTION | 23 | BB97 - 106 | 97 - 106 | 24 | X-RAY DIFFRACTION | 24 | BB107 - 124 | 107 - 124 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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