ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0352精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | MOLREP | | 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: 1X7F 解像度: 2.05→49.503 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.184 / SU B: 15.85 / SU ML: 0.195 / Average fsc free: 0.9454 / Average fsc work: 0.9632 / 交差検証法: FREE R-VALUE / ESU R: 0.229 / ESU R Free: 0.192 詳細: Hydrogens have been used if present in the input file
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2486 | 1716 | 2.5 % |
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Rwork | 0.2006 | 66914 | - |
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all | 0.202 | - | - |
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obs | - | 68630 | 96.216 % |
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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 BULK SOLVENT |
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原子変位パラメータ | Biso mean: 37.311 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.936 Å2 | 0.221 Å2 | -1.089 Å2 |
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2- | - | 2.483 Å2 | 1.892 Å2 |
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3- | - | - | -1.828 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.05→49.503 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8679 | 0 | 36 | 358 | 9073 |
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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_d0.004 | 0.012 | 8895 | X-RAY DIFFRACTION | r_angle_refined_deg1.126 | 1.636 | 12038 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.613 | 5 | 1120 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg11.515 | 10 | 55 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.358 | 10 | 1500 | X-RAY DIFFRACTION | r_dihedral_angle_6_deg13.693 | 10 | 385 | X-RAY DIFFRACTION | r_chiral_restr0.092 | 0.2 | 1352 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 6644 | X-RAY DIFFRACTION | r_nbd_refined0.221 | 0.2 | 3727 | X-RAY DIFFRACTION | r_nbtor_refined0.307 | 0.2 | 6130 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.147 | 0.2 | 448 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.213 | 0.2 | 106 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.146 | 0.2 | 29 | X-RAY DIFFRACTION | r_mcbond_it1.027 | 2.208 | 4489 | X-RAY DIFFRACTION | r_mcangle_it1.619 | 2.826 | 5606 | X-RAY DIFFRACTION | r_scbond_it1.764 | 2.651 | 4406 | X-RAY DIFFRACTION | r_scangle_it2.542 | 3.274 | 6432 | X-RAY DIFFRACTION | r_lrange_it6.131 | 19.914 | 13158 | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Rfactor all | Num. reflection all | Fsc free | Fsc work | % reflection obs (%) | WRfactor Rwork |
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2.05-2.103 | 0.339 | 125 | 0.327 | 4897 | 0.327 | 5296 | 0.913 | 0.916 | 94.8263 | 0.306 | 2.103-2.16 | 0.301 | 124 | 0.303 | 4813 | 0.303 | 5113 | 0.921 | 0.935 | 96.5578 | 0.277 | 2.16-2.223 | 0.34 | 121 | 0.28 | 4716 | 0.281 | 5003 | 0.912 | 0.948 | 96.682 | 0.254 | 2.223-2.291 | 0.292 | 116 | 0.268 | 4535 | 0.269 | 4867 | 0.938 | 0.951 | 95.5619 | 0.241 | 2.291-2.366 | 0.288 | 114 | 0.258 | 4429 | 0.259 | 4700 | 0.949 | 0.958 | 96.6596 | 0.228 | 2.366-2.449 | 0.289 | 109 | 0.251 | 4258 | 0.252 | 4515 | 0.942 | 0.96 | 96.722 | 0.222 | 2.449-2.541 | 0.323 | 105 | 0.256 | 4102 | 0.258 | 4410 | 0.909 | 0.955 | 95.3968 | 0.227 | 2.541-2.645 | 0.268 | 101 | 0.232 | 3960 | 0.232 | 4191 | 0.949 | 0.97 | 96.8981 | 0.199 | 2.645-2.762 | 0.291 | 99 | 0.211 | 3845 | 0.213 | 4063 | 0.945 | 0.975 | 97.0711 | 0.181 | 2.762-2.896 | 0.238 | 94 | 0.202 | 3669 | 0.203 | 3864 | 0.962 | 0.977 | 97.3861 | 0.177 | 2.896-3.052 | 0.226 | 89 | 0.205 | 3482 | 0.205 | 3689 | 0.968 | 0.976 | 96.8013 | 0.182 | 3.052-3.237 | 0.292 | 84 | 0.187 | 3269 | 0.19 | 3497 | 0.955 | 0.978 | 95.8822 | 0.172 | 3.237-3.459 | 0.289 | 79 | 0.187 | 3078 | 0.189 | 3286 | 0.953 | 0.979 | 96.0743 | 0.175 | 3.459-3.735 | 0.186 | 73 | 0.162 | 2829 | 0.163 | 3047 | 0.979 | 0.985 | 95.2412 | 0.158 | 3.735-4.089 | 0.178 | 66 | 0.159 | 2592 | 0.159 | 2787 | 0.978 | 0.986 | 95.3714 | 0.158 | 4.089-4.568 | 0.196 | 62 | 0.153 | 2393 | 0.154 | 2565 | 0.98 | 0.987 | 95.7115 | 0.157 | 4.568-5.267 | 0.231 | 53 | 0.155 | 2069 | 0.156 | 2232 | 0.971 | 0.986 | 95.0717 | 0.164 | 5.267-6.433 | 0.251 | 45 | 0.195 | 1786 | 0.197 | 1900 | 0.963 | 0.978 | 96.3684 | 0.2 | 6.433-9.021 | 0.203 | 36 | 0.16 | 1401 | 0.161 | 1473 | 0.972 | 0.985 | 97.556 | 0.175 | 9.021-49.503 | 0.212 | 21 | 0.167 | 790 | 0.168 | 826 | 0.974 | 0.985 | 98.184 | 0.205 |
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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 | 3.8673 | -0.1078 | -0.3161 | 3.3312 | 0.2941 | 3.69 | 0.0515 | 0.0308 | 0.31 | -0.0275 | -0.0746 | -0.1467 | -0.3705 | 0.0738 | 0.023 | 0.3771 | -0.0101 | 0.0662 | 0.0669 | 0.0323 | 0.2731 | 13.4351 | 15.929 | 19.6279 | 2 | 3.7741 | -0.9864 | -0.623 | 4.0774 | 3.2097 | 6.7932 | -0.1506 | -0.2836 | 0.1658 | 0.167 | 0.1535 | -0.1007 | -0.0214 | 0.4586 | -0.0029 | 0.3072 | 0.0036 | 0.0539 | 0.0937 | 0.0633 | 0.2417 | 13.3151 | 7.0995 | 21.0744 | 3 | 2.0841 | 1.0055 | -0.4452 | 2.1093 | -1.0185 | 1.6118 | 0.0232 | 0.0905 | 0.0628 | -0.0014 | -0.0271 | 0.008 | -0.074 | -0.014 | 0.0039 | 0.3 | -0.0087 | 0.0934 | 0.0087 | -0.0097 | 0.2289 | 27.1515 | 9.49 | -1.4281 | 4 | 3.6505 | -0.6525 | -3.8446 | 1.7508 | 1.4683 | 7.2223 | -0.0406 | 0.2434 | 0.0467 | -0.1542 | -0.0023 | 0.2301 | -0.1044 | -0.4996 | 0.0429 | 0.2982 | -0.0271 | 0.0068 | 0.154 | -0.002 | 0.3052 | 14.0953 | 1.0468 | 2.4673 | 5 | 2.9884 | -1.3958 | 0.6198 | 3.5117 | 0.2289 | 3.5556 | -0.1463 | -0.2914 | 0.032 | 0.2102 | 0.1166 | -0.2059 | -0.0993 | 0.0185 | 0.0296 | 0.3858 | 0.0153 | 0.0546 | 0.09 | -0.0169 | 0.3123 | 64.3085 | 31.6421 | 3.387 | 6 | 4.4557 | -4.2131 | -1.0352 | 7.2211 | 6.0903 | 8.3302 | -0.0466 | -0.031 | 0.0574 | -0.2342 | 0.063 | -0.035 | -0.3701 | 0.0308 | -0.0164 | 0.333 | -0.0517 | 0.042 | 0.1015 | 0.0585 | 0.2353 | 62.7794 | 27.4025 | -9.8231 | 7 | 2.3091 | 0.4394 | -1.572 | 1.2129 | -1.1522 | 3.2183 | -0.0287 | -0.0951 | -0.1131 | 0.0306 | -0.0176 | -0.0511 | 0.0557 | 0.1574 | 0.0463 | 0.2822 | -0.0473 | 0.0521 | 0.042 | -0.0034 | 0.2336 | 49.5434 | 9.3256 | -1.0011 | 8 | 3.9572 | 3.5122 | 1.1967 | 6.1823 | 1.5703 | 1.0146 | -0.1027 | 0.2182 | -0.2718 | 0.0358 | 0.2061 | -0.4856 | 0.0238 | 0.2141 | -0.1034 | 0.3616 | 0.0102 | 0.0929 | 0.1513 | -0.011 | 0.2793 | 65.3299 | 16.0389 | -10.891 | 9 | 2.2466 | 0.1728 | -0.8458 | 5.8177 | 0.3875 | 2.7157 | -0.0191 | -0.2398 | -0.3613 | 0.2145 | -0.0536 | 0.0561 | 0.4204 | 0.1301 | 0.0727 | 0.4461 | 0.043 | 0.049 | 0.1857 | 0.0107 | 0.297 | -2.5449 | 32.217 | 32.3075 | 10 | 2.4325 | -1.0016 | 2.3212 | 0.9244 | -1.5349 | 2.8791 | 0.0022 | 0.1314 | -0.0155 | -0.0642 | 0.0302 | 0.0642 | 0.0982 | 0.0306 | -0.0324 | 0.3629 | -0.0091 | 0.1042 | 0.1221 | 0.0287 | 0.2407 | 11.8035 | 49.2744 | 38.8418 | 11 | 11.7939 | 10.1245 | -1.6645 | 13.1379 | 0.6169 | 1.1875 | 0.3784 | -0.502 | 0.274 | 0.6386 | -0.2134 | -0.0199 | 0.0307 | 0.1323 | -0.1651 | 0.4627 | 0.0641 | 0.0313 | 0.362 | 0.0361 | 0.2138 | 15.3939 | 49.9916 | 64.8951 | 12 | 1.9066 | -0.5096 | 1.9491 | 0.4098 | -0.277 | 2.2835 | -0.0292 | -0.1963 | -0.0398 | 0.065 | 0.0563 | 0.1239 | -0.1079 | -0.2485 | -0.0271 | 0.4011 | 0.0167 | 0.1348 | 0.125 | 0.0364 | 0.241 | 7.082 | 50.9946 | 44.0233 | 13 | 10.7326 | 1.6895 | 1.0217 | 6.4323 | 1.4255 | 6.4166 | -0.1271 | 0.2675 | 0.0645 | -0.397 | -0.0488 | 0.0266 | 0.1178 | -0.1685 | 0.1758 | 0.4267 | -0.0287 | 0.0728 | 0.2228 | 0.0271 | 0.2586 | 55.8782 | 35.3406 | 56.1495 | 14 | 6.8455 | -1.819 | -0.4926 | 3.1525 | -2.0959 | 3.0041 | 0.1919 | 0.0948 | -0.7758 | -0.5279 | -0.0853 | 0.5162 | 0.6895 | -0.4511 | -0.1066 | 0.7894 | -0.1336 | -0.0125 | 0.4833 | -0.0693 | 0.4503 | 47.1947 | 26.027 | 52.7667 | 15 | 1.5885 | -0.3564 | 0.3171 | 5.254 | -1.7904 | 4.4836 | -0.0461 | 0.1301 | -0.2038 | -0.1843 | 0.1795 | 0.2494 | 0.4597 | -0.315 | -0.1334 | 0.4018 | -0.0701 | 0.0758 | 0.2224 | 0.0238 | 0.2642 | 48.1872 | 32.749 | 63.5653 | 16 | 2.1564 | -0.179 | 0.9669 | 0.9259 | -0.4705 | 1.9393 | -0.0188 | 0.0541 | 0.0674 | -0.0819 | -0.1244 | -0.107 | -0.0603 | 0.1756 | 0.1432 | 0.3897 | 0.0217 | 0.1245 | 0.1271 | 0.0629 | 0.242 | 36.5087 | 50.235 | 47.2991 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA2 - 81 | 2 | X-RAY DIFFRACTION | 2 | ALLA82 - 105 | 3 | X-RAY DIFFRACTION | 3 | ALLA106 - 249 | 4 | X-RAY DIFFRACTION | 4 | ALLA250 - 278 | | | | | | | | |
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