ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALA | 3.3.20データスケーリング | | PHENIX | 1.8.1_1168精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | MOSFLM | | データ削減 | | 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: PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8 解像度: 1.6→31.598 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8981 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / 位相誤差: 17.48 / 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 | 0.1809 | 5138 | 4.98 % | RANDOM |
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Rwork | 0.1469 | - | - | - |
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all | 0.1486 | 103114 | - | - |
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obs | 0.1486 | 103114 | 96.99 % | - |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 77.46 Å2 / Biso mean: 20.1631 Å2 / Biso min: 5.14 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→31.598 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6517 | 0 | 0 | 1073 | 7590 |
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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_d0.009 | 6708 | X-RAY DIFFRACTION | f_angle_d1.276 | 9141 | X-RAY DIFFRACTION | f_chiral_restr0.075 | 976 | X-RAY DIFFRACTION | f_plane_restr0.008 | 1209 | X-RAY DIFFRACTION | f_dihedral_angle_d12.611 | 2434 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.6-1.6182 | 0.2335 | 186 | 0.2175 | 3378 | 3564 | 100 | 1.6182-1.6372 | 0.2574 | 173 | 0.2123 | 3298 | 3471 | 100 | 1.6372-1.6572 | 0.2372 | 171 | 0.2022 | 3374 | 3545 | 100 | 1.6572-1.6782 | 0.2222 | 188 | 0.1903 | 3337 | 3525 | 100 | 1.6782-1.7002 | 0.2325 | 163 | 0.1938 | 3331 | 3494 | 100 | 1.7002-1.7235 | 0.2123 | 181 | 0.1905 | 3381 | 3562 | 100 | 1.7235-1.7482 | 0.2342 | 175 | 0.1877 | 3303 | 3478 | 100 | 1.7482-1.7742 | 0.2242 | 190 | 0.1736 | 3385 | 3575 | 100 | 1.7742-1.802 | 0.2007 | 157 | 0.1676 | 3354 | 3511 | 100 | 1.802-1.8315 | 0.218 | 188 | 0.1699 | 3330 | 3518 | 100 | 1.8315-1.8631 | 0.2226 | 179 | 0.1683 | 3282 | 3461 | 100 | 1.8631-1.897 | 0.2143 | 182 | 0.1715 | 3340 | 3522 | 99 | 1.897-1.9334 | 0.2531 | 163 | 0.2085 | 3248 | 3411 | 96 | 1.9334-1.9729 | 0.2006 | 179 | 0.1682 | 3285 | 3464 | 98 | 1.9729-2.0158 | 0.2032 | 179 | 0.1581 | 3314 | 3493 | 99 | 2.0158-2.0627 | 0.1851 | 164 | 0.1532 | 3321 | 3485 | 98 | 2.0627-2.1142 | 0.1872 | 169 | 0.1639 | 3229 | 3398 | 96 | 2.1142-2.1714 | 0.1852 | 163 | 0.1407 | 3315 | 3478 | 99 | 2.1714-2.2353 | 0.1779 | 176 | 0.1408 | 3299 | 3475 | 98 | 2.2353-2.3074 | 0.2087 | 164 | 0.1565 | 3158 | 3322 | 93 | 2.3074-2.3898 | 0.171 | 195 | 0.1338 | 3223 | 3418 | 97 | 2.3898-2.4855 | 0.1603 | 157 | 0.1316 | 3260 | 3417 | 96 | 2.4855-2.5986 | 0.186 | 160 | 0.129 | 3239 | 3399 | 96 | 2.5986-2.7355 | 0.1668 | 174 | 0.136 | 3162 | 3336 | 94 | 2.7355-2.9068 | 0.1578 | 167 | 0.1328 | 3211 | 3378 | 95 | 2.9068-3.131 | 0.1734 | 173 | 0.1311 | 3165 | 3338 | 93 | 3.131-3.4458 | 0.1495 | 151 | 0.1309 | 3086 | 3237 | 92 | 3.4458-3.9436 | 0.1513 | 152 | 0.1179 | 3063 | 3215 | 90 | 3.9436-4.9654 | 0.1393 | 168 | 0.1125 | 3101 | 3269 | 91 | 4.9654-31.6037 | 0.1539 | 151 | 0.1491 | 3204 | 3355 | 92 |
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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 | 2.156 | 0.0528 | 0.2923 | 1.6162 | -0.4735 | 0.9357 | 0.0403 | 0.0339 | 0.4298 | -0.0148 | -0.014 | -0.0252 | -0.4361 | 0.027 | -0.0007 | 0.232 | 0.0304 | 0.0307 | 0.0854 | -0.0043 | 0.1582 | -10.0052 | 52.394 | 82.9991 | 2 | 0.9969 | -0.8656 | 0.3232 | 1.159 | 0.3857 | 1.2582 | 0.0264 | 0.0074 | 0.2218 | 0.0736 | 0.155 | -0.5811 | -0.1384 | 0.5825 | 0.0918 | 0.1193 | -0.0304 | -0.0313 | 0.2579 | -0.0743 | 0.2495 | 5.4195 | 40.0813 | 92.6973 | 3 | 0.7982 | -0.2774 | -0.0819 | 0.7624 | -0.0722 | 1.0049 | 0.0185 | -0.0664 | 0.1608 | 0.1051 | 0.0277 | -0.1311 | -0.2091 | 0.1378 | -0.065 | 0.1332 | -0.0127 | -0.0055 | 0.1022 | -0.0425 | 0.1117 | -5.2076 | 43.8559 | 93.2583 | 4 | 1.0193 | -1.0766 | -0.2218 | 2.1566 | 0.7141 | 0.9175 | -0.2153 | -0.2737 | -0.2156 | 0.286 | 0.1008 | 0.1928 | 0.3147 | 0.1868 | 0.1023 | 0.1832 | 0.0549 | 0.018 | 0.1169 | 0.0104 | 0.1189 | -9.9493 | 26.4396 | 101.1372 | 5 | 0.826 | -0.538 | -0.4844 | 0.437 | 0.4993 | 1.0217 | -0.0605 | 0.0333 | -0.1237 | 0.0421 | -0.0071 | 0.0288 | 0.2422 | 0.0749 | 0.0474 | 0.1285 | 0.0181 | 0.009 | 0.0988 | -0.0185 | 0.0951 | -7.9068 | 25.4721 | 89.0795 | 6 | 0.3465 | 0.0365 | -0.3963 | 0.4671 | 0.3638 | 1.4764 | -0.0202 | 0.0248 | -0.1157 | -0.036 | -0.058 | 0.0238 | 0.1332 | -0.0221 | 0.0361 | 0.122 | 0.0119 | -0.0137 | 0.0892 | -0.0305 | 0.1039 | -11.0319 | 24.9342 | 80.1705 | 7 | 0.9184 | 0.2282 | -0.2037 | 0.6729 | -0.0314 | 1.0316 | -0.0308 | 0.1815 | -0.0497 | -0.1726 | -0.0717 | 0.0792 | 0.2114 | -0.0804 | 0.0897 | 0.1504 | 0.0099 | -0.0054 | 0.1292 | -0.0333 | 0.1158 | -13.7187 | 28.7894 | 73.9627 | 8 | 0.5446 | 0.0339 | -0.3955 | 0.4415 | -0.1733 | 0.9319 | 0.1059 | 0.1564 | 0.0146 | -0.0745 | -0.1038 | -0.0075 | -0.0828 | -0.0629 | 0.023 | 0.1075 | 0.0322 | -0.0016 | 0.1249 | 0.004 | 0.0693 | -9.945 | 38.9603 | 71.197 | 9 | 0.7581 | 0.2163 | 0.2531 | 1.4129 | -0.0815 | 1.4257 | 0.1364 | 0.1576 | 0.1456 | -0.0851 | -0.0633 | -0.12 | -0.24 | 0.1225 | -0.0575 | 0.1476 | 0.02 | 0.0449 | 0.1121 | 0.002 | 0.1274 | -5.664 | 45.9827 | 77.9166 | 10 | 0.5625 | 0.026 | 0.5422 | 0.7019 | -0.6619 | 2.0622 | 0.1342 | 0.0836 | 0.0564 | -0.0297 | -0.05 | 0.1335 | -0.2664 | -0.3036 | -0.0959 | 0.1105 | 0.0711 | 0.011 | 0.1519 | -0.0014 | 0.1084 | -21.3787 | 43.9196 | 83.2587 | 11 | 1.4783 | 0.2048 | 0.4762 | 0.4804 | 0.056 | 0.6612 | 0.0079 | -0.0712 | -0.3438 | 0.1528 | -0.0118 | -0.2941 | 0.3009 | 0.4699 | -0.1537 | 0.1371 | 0.0635 | -0.0473 | 0.3233 | 0.0532 | 0.1951 | 18.9826 | 32.5617 | 53.7597 | 12 | 0.6258 | 0.6152 | 0.1364 | 0.9726 | -0.0736 | 0.6339 | -0.2108 | 0.0884 | -0.3657 | -0.2926 | 0.0558 | -0.2241 | 0.2913 | 0.0411 | 0.0069 | 0.1868 | -0.0081 | 0.0545 | 0.0717 | -0.0043 | 0.2045 | 2.4887 | 25.1063 | 44.4595 | 13 | 0.9575 | 0.0818 | 0.0109 | 0.4948 | 0.222 | 0.8332 | -0.1653 | -0.1396 | -0.2518 | 0.1032 | -0.0119 | 0.0092 | 0.4067 | 0.1258 | 0.0078 | 0.1403 | 0.0391 | 0.0264 | 0.097 | 0.0621 | 0.1408 | 4.5396 | 29.7389 | 53.1861 | 14 | 1.0663 | -0.0637 | 0.3553 | 0.2933 | 0.0527 | 3.8349 | -0.1357 | 0.0017 | -0.2125 | 0.1034 | 0.0145 | 0.2288 | -0.0795 | -0.6565 | 0.0424 | 0.0996 | 0.0093 | 0.0341 | 0.182 | 0.0128 | 0.1991 | -13.4489 | 37.8337 | 52.4904 | 15 | 0.6186 | 0.1248 | -0.2386 | 0.5911 | 0.0815 | 1.7218 | -0.1127 | 0.0643 | -0.0895 | -0.0454 | 0.0136 | 0.1271 | -0.0186 | -0.2646 | 0.0716 | 0.0885 | 0.0111 | -0.0077 | 0.0819 | -0.0014 | 0.1049 | -6.2575 | 42.0842 | 43.6907 | 16 | 0.3729 | 0.1422 | -0.4059 | 0.5798 | -0.398 | 1.0816 | 0.0608 | 0.1245 | 0.0081 | -0.1204 | -0.0198 | 0.0109 | -0.2113 | -0.1692 | -0.0512 | 0.1611 | 0.0417 | -0.0056 | 0.096 | 0.0147 | 0.0855 | -0.9243 | 49.3578 | 40.4052 | 17 | 0.7956 | -0.2204 | -0.2523 | 0.3703 | 0.209 | 0.6812 | 0.0482 | 0.0374 | 0.0616 | -0.1017 | -0.0028 | -0.0601 | -0.2425 | 0.1326 | -0.021 | 0.1321 | -0.0359 | 0.0155 | 0.0745 | -0.003 | 0.0917 | 11.2757 | 49.089 | 40.6516 | 18 | 1.4283 | -0.0608 | -0.1043 | 1.1787 | -0.3707 | 0.8657 | -0.0984 | -0.0521 | -0.2106 | -0.1158 | 0.0921 | -0.116 | 0.0663 | 0.366 | 0.0004 | 0.0946 | 0.0126 | 0.0208 | 0.1683 | 0.0016 | 0.1246 | 16.4141 | 36.3471 | 45.5641 | 19 | 1.3434 | 0.1089 | -0.1308 | 1.0387 | -0.2761 | 0.1221 | -0.0419 | -0.398 | 0.0197 | 0.2042 | 0.1132 | -0.0711 | -0.1353 | 0.3662 | -0.0315 | 0.1042 | -0.0207 | -0.0259 | 0.2212 | -0.0285 | 0.066 | 11.985 | 46.6636 | 58.0202 | 20 | 1.4126 | -0.0455 | 0.0634 | 2.4577 | 0.074 | 1.4363 | 0.0253 | -0.2207 | -0.0628 | 0.1378 | 0.0165 | -0.2328 | 0.2096 | 0.5452 | 0.0087 | 0.0771 | 0.0497 | -0.0255 | 0.2889 | 0.0114 | 0.1042 | 21.183 | 1.3207 | 85.2878 | 21 | 1.3175 | -0.7644 | -0.6603 | 0.7912 | 0.3203 | 0.416 | -0.0145 | -0.2179 | 0.1199 | 0.1081 | 0.0638 | -0.109 | -0.3198 | 0.2545 | -0.0068 | 0.3197 | -0.1742 | 0.0592 | 0.4239 | -0.1325 | 0.2897 | 20.6216 | 21.4254 | 89.4288 | 22 | 0.4526 | 0.0857 | -0.4377 | 0.3962 | -0.0691 | 1.0436 | 0.1094 | -0.4171 | 0.1387 | 0.0738 | 0.0013 | -0.2225 | -0.1113 | 0.8924 | 0.2819 | 0.0068 | -0.0223 | -0.0314 | 0.3622 | -0.0301 | 0.1343 | 23.3985 | 9.2779 | 82.5153 | 23 | 2.215 | -1.576 | -0.7217 | 1.9784 | 0.4373 | 1.5798 | 0.3839 | 0.1909 | 0.4083 | -0.2703 | -0.2409 | -0.1647 | -0.4536 | 0.3077 | 0.0472 | 0.1772 | -0.0051 | 0.0524 | 0.1314 | 0.0419 | 0.1752 | 15.9536 | 19.0636 | 66.921 | 24 | 0.9634 | -0.3591 | -0.7953 | 0.8127 | 0.3381 | 1.4477 | 0.0937 | 0.018 | 0.1056 | -0.089 | -0.0908 | 0.0685 | -0.2807 | 0.0241 | 0.0376 | 0.1207 | -0.0075 | 0.0082 | 0.0808 | -0.0062 | 0.1123 | 7.2189 | 15.807 | 74.8705 | 25 | 1.7375 | -0.0365 | -0.9147 | 0.3093 | -0.0322 | 1.7283 | 0.0513 | 0.0374 | -0.0651 | -0.0527 | -0.0222 | 0.0868 | -0.0754 | -0.1141 | -0.0246 | 0.0901 | 0.0103 | -0.001 | 0.0573 | -0.0011 | 0.0976 | -0.0044 | 9.7241 | 77.2436 | 26 | 0.5118 | -0.026 | -0.231 | 0.4498 | -0.2045 | 1.2881 | 0.0125 | -0.016 | -0.0495 | -0.0493 | 0.0082 | 0.0304 | 0.1008 | -0.046 | -0.02 | 0.0881 | -0.0097 | -0.0084 | 0.0786 | 0.0032 | 0.093 | 1.2197 | 2.3423 | 84.2817 | 27 | 0.8188 | 0.1628 | -0.4107 | 0.4225 | -0.4878 | 1.0384 | -0.0639 | -0.1809 | -0.1083 | -0.0483 | -0.0586 | -0.0863 | 0.3359 | 0.3032 | 0.0459 | 0.1272 | 0.0464 | 0.0045 | 0.1351 | 0.0131 | 0.1119 | 11.7165 | -3.5332 | 84.864 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | CHAIN A AND (RESID 6:25 )A0 | 2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESID 26:49 )A0 | 3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESID 50:95 )A0 | 4 | X-RAY DIFFRACTION | 4 | CHAIN A AND (RESID 96:111 )A0 | 5 | X-RAY DIFFRACTION | 5 | CHAIN A AND (RESID 112:141 )A0 | 6 | X-RAY DIFFRACTION | 6 | CHAIN A AND (RESID 142:163 )A0 | 7 | X-RAY DIFFRACTION | 7 | CHAIN A AND (RESID 164:197 )A0 | 8 | X-RAY DIFFRACTION | 8 | CHAIN A AND (RESID 198:230 )A0 | 9 | X-RAY DIFFRACTION | 9 | CHAIN A AND (RESID 231:265 )A0 | 10 | X-RAY DIFFRACTION | 10 | CHAIN A AND (RESID 266:289 )A0 | 11 | X-RAY DIFFRACTION | 11 | CHAIN B AND (RESID 4:23 )B0 | 12 | X-RAY DIFFRACTION | 12 | CHAIN B AND (RESID 24:49 )B0 | 13 | X-RAY DIFFRACTION | 13 | CHAIN B AND (RESID 50:95 )B0 | 14 | X-RAY DIFFRACTION | 14 | CHAIN B AND (RESID 96:111 )B0 | 15 | X-RAY DIFFRACTION | 15 | CHAIN B AND ( | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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