ソフトウェア | 名称 | バージョン | 分類 |
---|
PHENIX | 1.14_3260精密化 | XDS | | データ削減 | XDS | | データスケーリング | PHASER | | 位相決定 | |
|
---|
精密化 | 構造決定の手法: 分子置換 開始モデル: 5VYE 解像度: 1.75→48.48 Å / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 20.02 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.19 | 1998 | 1.34 % |
---|
Rwork | 0.1707 | 147232 | - |
---|
obs | 0.171 | 149230 | 99.83 % |
---|
|
---|
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 |
---|
原子変位パラメータ | Biso max: 98.41 Å2 / Biso mean: 28.7257 Å2 / Biso min: 12.59 Å2 |
---|
精密化ステップ | サイクル: final / 解像度: 1.75→48.48 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 10016 | 0 | 0 | 1288 | 11304 |
---|
Biso mean | - | - | - | 37.98 | - |
---|
残基数 | - | - | - | - | 1336 |
---|
|
---|
Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | Rms | タイプ |
---|
1 | 1 | A4092 | X-RAY DIFFRACTION | 2.635 | TORSIONAL1 | 2 | B4092 | X-RAY DIFFRACTION | 2.635 | TORSIONAL1 | 3 | C4092 | X-RAY DIFFRACTION | 2.635 | TORSIONAL1 | 4 | D4092 | X-RAY DIFFRACTION | 2.635 | TORSIONAL | | | | | | | |
|
---|
LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
---|
1.75-1.7938 | 0.2253 | 156 | 0.2048 | 10384 | 100 | 1.7938-1.8423 | 0.2217 | 119 | 0.1973 | 10456 | 100 | 1.8423-1.8965 | 0.2379 | 157 | 0.1962 | 10421 | 100 | 1.8965-1.9577 | 0.2532 | 138 | 0.2231 | 10363 | 99 | 1.9577-2.0277 | 0.2236 | 129 | 0.1887 | 10431 | 100 | 2.0277-2.1088 | 0.2026 | 153 | 0.194 | 10410 | 100 | 2.1088-2.2048 | 0.2368 | 139 | 0.1784 | 10489 | 100 | 2.2048-2.3211 | 0.2264 | 141 | 0.1872 | 10409 | 99 | 2.3211-2.4665 | 0.2123 | 145 | 0.1733 | 10513 | 100 | 2.4665-2.6569 | 0.1883 | 137 | 0.1709 | 10494 | 100 | 2.6569-2.9243 | 0.2003 | 146 | 0.1818 | 10575 | 100 | 2.9243-3.3473 | 0.1948 | 147 | 0.1661 | 10584 | 100 | 3.3473-4.2169 | 0.1516 | 145 | 0.1444 | 10680 | 100 | 4.2169-48.336 | 0.1538 | 146 | 0.1568 | 11023 | 100 |
|
---|
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) |
---|
1 | 0.4315 | -0.1635 | 0.1091 | 0.6604 | 0.1236 | 2.3826 | -0 | 0.0332 | -0.0724 | -0.0762 | 0.0759 | -0.1418 | 0.0877 | 0.3229 | -0.0246 | 0.191 | 0.0025 | 0.0286 | 0.1789 | -0.0149 | 0.2418 | 2.6472 | -18.3907 | 36.1812 | 2 | 0.7217 | 0.1156 | 0.4052 | 0.509 | 0.0197 | 0.9027 | -0.0228 | 0.0097 | 0.0463 | 0.0438 | 0.0066 | -0.0452 | -0.0701 | 0.109 | 0.0204 | 0.167 | -0.0219 | -0.0011 | 0.159 | -0.0101 | 0.1911 | -2.7271 | 0.8499 | 34.9014 | 3 | 1.1028 | -0.3858 | -0.6188 | 0.4899 | 0.5106 | 0.682 | 0.0224 | 0.1541 | 0.0847 | -0.1764 | -0.0162 | -0.0367 | -0.1247 | -0.0554 | 0.0057 | 0.21 | -0.0014 | -0.0137 | 0.1687 | 0.0171 | 0.1726 | -12.1661 | 6.5328 | 21.5769 | 4 | 0.3879 | -0.2576 | 0.1577 | 1.4796 | 0.7374 | 0.6085 | -0.0207 | 0.1105 | 0.0361 | -0.0905 | 0.0107 | -0.0454 | -0.0727 | 0.086 | 0.0069 | 0.1747 | -0.0363 | 0.0213 | 0.1877 | 0.0048 | 0.1879 | 1.335 | 1.7216 | 24.3245 | 5 | 0.1977 | -0.1553 | -0.0835 | 0.4638 | 0.017 | 0.8696 | -0.0226 | 0.0278 | -0.0343 | -0.0592 | 0.0077 | -0.0674 | 0.0411 | 0.1642 | 0.0055 | 0.1652 | -0.0126 | 0.0156 | 0.1723 | -0.0065 | 0.2026 | 1.2619 | -7.7643 | 30.4695 | 6 | 1.1893 | 0.0003 | -0.2181 | 1.8146 | -0.3754 | 1.8898 | 0.0287 | 0.1304 | -0.0211 | -0.3941 | -0.0971 | 0.3957 | 0.2001 | -0.3137 | 0.0347 | 0.3217 | -0.0061 | -0.0232 | 0.2821 | -0.0495 | 0.2387 | -8.5431 | -15.2901 | 5.8613 | 7 | 0.8616 | 0.1103 | 0.1014 | 0.5777 | -0.1534 | 1.7736 | -0.0041 | 0.0697 | -0.0664 | -0.0689 | 0.0009 | 0.0482 | 0.1906 | -0.1968 | -0.0327 | 0.3094 | -0.0188 | 0.0281 | 0.2566 | -0.0441 | 0.2265 | -5.5513 | -19.3228 | 11.1385 | 8 | 0.4915 | -0.3739 | 0.3431 | 0.8105 | -0.1936 | 2.2961 | 0.0641 | 0.0516 | -0.1288 | -0.1325 | -0.0161 | -0.0121 | 0.134 | 0.092 | -0.0162 | 0.1458 | -0.0012 | 0.0215 | 0.136 | -0.0089 | 0.1955 | -3.1087 | -24.1192 | 40.1845 | 9 | 0.8059 | 0.18 | 0.1724 | 0.3744 | 0.1847 | 1.3951 | -0.0242 | 0.0149 | -0.1004 | -0.0705 | 0.0035 | 0.0121 | 0.1193 | -0.104 | 0.0052 | 0.1761 | -0.0258 | 0.0053 | 0.1557 | 0.0017 | 0.1993 | -22.1359 | -18.2372 | 42.0399 | 10 | 0.7889 | -0.1954 | 0.3509 | 1.1185 | -0.3907 | 0.5307 | -0.076 | -0.2068 | -0.0033 | 0.1438 | 0.0824 | 0.076 | -0.0816 | -0.2351 | -0.0089 | 0.1511 | 0.0309 | 0.0288 | 0.225 | -0.0059 | 0.1603 | -27.3219 | -9.0097 | 55.7989 | 11 | 1.3513 | -0.3328 | 0.7404 | 0.7323 | 0.1547 | 0.3838 | -0.0177 | -0.0836 | -0.0852 | 0.0446 | 0.029 | 0.0461 | 0.113 | -0.1303 | -0.0211 | 0.1638 | -0.0155 | 0.0066 | 0.1877 | 0.0229 | 0.2094 | -22.8983 | -22.5367 | 52.5054 | 12 | 0.7705 | 0.5328 | -0.4044 | 0.6581 | -0.349 | 0.9972 | 0.0478 | -0.0676 | -0.0678 | -0.0335 | 0.0324 | 0.0282 | 0.0328 | -0.0466 | -0.0659 | 0.1528 | -0.0012 | -0.0025 | 0.1421 | 0.0032 | 0.1796 | -21.5467 | -15.8895 | 36.6965 | 13 | 0.4895 | 0.0035 | 0.4868 | 0.9872 | -0.505 | 0.9558 | 0.0458 | -0.0259 | -0.0973 | 0.021 | 0.0019 | -0.0191 | 0.304 | -0.0301 | -0.0476 | 0.1823 | 0.03 | 0.0003 | 0.1538 | 0.004 | 0.2083 | -7.3897 | -27.4162 | 53.3047 | 14 | 1.8838 | -0.6622 | -0.6909 | 1.6596 | -0.0415 | 2.7508 | -0.0098 | -0.3453 | 0.6147 | 0.3521 | 0.0785 | -0.2037 | -0.4942 | 0.2966 | -0.1389 | 0.3152 | -0.0135 | -0.0394 | 0.2793 | -0.0599 | 0.2984 | -5.2843 | -13.6286 | 70.7681 | 15 | 1.7358 | -0.1843 | -0.1461 | 2.1655 | 0.258 | 2.2092 | -0.0213 | -0.2878 | 0.1843 | 0.2175 | 0.0216 | -0.1853 | -0.2576 | 0.1636 | -0.0136 | 0.2598 | -0.0102 | -0.0276 | 0.2326 | 0.0025 | 0.2034 | -1.2965 | -16.2318 | 65.4861 | 16 | 0.8474 | -0.3005 | -0.1715 | 0.8378 | -0.6313 | 1.8736 | -0.101 | -0.2082 | 0.1927 | 0.21 | 0.1425 | 0.1093 | -0.2605 | -0.258 | -0.018 | 0.2624 | 0.1068 | -0.0391 | 0.3227 | -0.0417 | 0.2635 | -48.6415 | 24.5574 | 35.7524 | 17 | 0.9401 | -0.2391 | 0.0338 | 0.4341 | -0.2616 | 1.1353 | -0.037 | -0.026 | -0.0325 | 0.009 | 0.0017 | 0.1737 | -0.024 | -0.2513 | 0.0369 | 0.1697 | 0.0165 | -0.013 | 0.2412 | -0.0269 | 0.2503 | -42.197 | 6.464 | 30.0817 | 18 | 1.1111 | -0.7042 | 0.2904 | 0.7877 | -0.2637 | 0.7539 | 0.0564 | 0.2006 | 0.0024 | -0.1822 | -0.1022 | 0.02 | -0.0166 | -0.0543 | 0.0401 | 0.2019 | 0.0169 | -0.0042 | 0.1999 | -0.0105 | 0.1749 | -29.1227 | 4.8332 | 18.7936 | 19 | 0.8919 | -0.3973 | -0.189 | 1.1861 | -0.357 | 0.2376 | 0.0223 | 0.1261 | -0.0121 | -0.1598 | -0.0075 | 0.1179 | -0.0434 | -0.1326 | 0.0043 | 0.2086 | 0.0314 | -0.0467 | 0.2663 | -0.0281 | 0.2325 | -43.0489 | 9.1654 | 19.076 | 20 | 0.7229 | 0.1296 | 0.4946 | 0.4204 | 0.0549 | 1.2166 | -0.0452 | -0.0683 | 0.0431 | -0.0331 | 0.0388 | 0.0565 | -0.0039 | -0.1459 | 0.0047 | 0.1619 | 0.0348 | -0.0159 | 0.2119 | -0.0141 | 0.2075 | -41.6151 | 5.257 | 35.776 | 21 | 1.0494 | -0.2698 | 0.3583 | 1.0008 | -0.6849 | 0.9178 | -0.0481 | 0.0524 | 0.1488 | -0.0496 | 0.0134 | 0.1084 | -0.0422 | -0.1172 | 0.0779 | 0.2119 | 0.081 | -0.0335 | 0.2628 | -0.0199 | 0.2787 | -47.6795 | 24.4578 | 21.5107 | 22 | 1.9321 | -1.0686 | -0.7328 | 1.2637 | 0.1757 | 3.2227 | 0.1857 | 0.0632 | 0.3775 | 0.0397 | -0.1389 | -0.6566 | -0.4037 | 0.6997 | -0.0978 | 0.3179 | -0.0135 | -0.0319 | 0.4337 | 0.0708 | 0.4479 | -29.093 | 30.5998 | 10.5857 | 23 | 3.1995 | -0.2606 | -0.4374 | 1.9311 | -0.0455 | 2.4072 | 0.1459 | -0.02 | 0.4167 | -0.0683 | -0.1673 | -0.3028 | -0.2813 | 0.5318 | 0.0692 | 0.312 | 0.0223 | -0.0389 | 0.3508 | 0.0488 | 0.3667 | -33.5007 | 33.0482 | 15.8035 | 24 | 1.0621 | 0.1828 | -0.4734 | 0.8092 | -0.6405 | 2.0908 | -0.0458 | -0.133 | 0.2927 | 0.191 | 0.0528 | 0.0512 | -0.4345 | -0.3088 | 0.0103 | 0.3382 | 0.1642 | -0.0391 | 0.3688 | -0.0774 | 0.3223 | -44.4878 | 28.4095 | 43.0327 | 25 | 0.5859 | -0.1461 | 0.0867 | 0.6325 | -0.5134 | 0.7871 | -0.1955 | -0.1063 | 0.2692 | 0.2478 | 0.0365 | -0.1327 | -0.3923 | -0.1584 | 0.1255 | 0.3141 | 0.0838 | -0.0801 | 0.188 | -0.0676 | 0.2615 | -26.5522 | 21.2262 | 48.1674 | 26 | 1.0438 | -0.4035 | 0.2611 | 0.8834 | 0.2437 | 1.1256 | -0.1977 | -0.3399 | 0.1416 | 0.2138 | 0.0901 | -0.0033 | -0.1587 | -0.2086 | 0.0955 | 0.2295 | 0.0795 | -0.0203 | 0.2242 | -0.0362 | 0.1658 | -25.0394 | 7.8401 | 59.044 | 27 | 1.0318 | -0.1857 | -0.6025 | 0.9464 | -0.1848 | 0.4043 | -0.2598 | -0.2329 | 0.2807 | 0.2805 | 0.0478 | -0.0655 | -0.3574 | -0.2498 | 0.0687 | 0.3837 | 0.1579 | -0.0802 | 0.2908 | -0.1342 | 0.2609 | -28.9594 | 21.9315 | 59.2417 | 28 | 0.4838 | 0.4369 | 0.6088 | 0.4909 | 0.0959 | 1.4976 | -0.112 | -0.1454 | 0.1299 | 0.127 | -0.0051 | -0.0288 | -0.1166 | -0.0849 | 0.1171 | 0.2542 | 0.0546 | -0.0552 | 0.1954 | -0.0489 | 0.2603 | -25.506 | 20.7587 | 42.4135 | 29 | 0.4819 | 0.2972 | -0.2599 | 0.0539 | 0.0693 | 0.9098 | 0.0416 | -0.0912 | 0.2204 | 0.2645 | 0.0016 | 0.0287 | -0.6733 | -0.4031 | -0.0938 | 0.4138 | 0.2238 | -0.0326 | 0.4094 | -0.0926 | 0.3306 | -44.0739 | 27.1081 | 57.3018 | 30 | 1.5 | -0.3006 | 0.8728 | 1.3521 | -0.4578 | 2.4651 | -0.1278 | -0.1781 | -0.3781 | -0.0459 | -0.0103 | -0.0139 | 0.5003 | -0.4647 | 0.0765 | 0.4425 | 0.1284 | 0.068 | 0.6202 | -0.0882 | 0.3145 | -50.6601 | 8.3861 | 67.9956 | 31 | 0.6275 | 0.3961 | -0.2559 | 1.6283 | -0.4263 | 1.5701 | -0.0146 | 0.0939 | -0.07 | -0.1134 | -0.0789 | 0.1853 | 0.2452 | -0.5222 | 0.0917 | 0.3863 | 0.139 | 0.0143 | 0.6171 | -0.0998 | 0.28 | -53.0383 | 13.0166 | 62.8651 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 6 through 39 )A6 - 39 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 40 through 87 )A40 - 87 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 88 through 154 )A88 - 154 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 155 through 212 )A155 - 212 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 213 through 276 )A213 - 276 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 277 through 304 )A277 - 304 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 305 through 339 )A305 - 339 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 6 through 39 )B6 - 39 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 40 through 87 )B40 - 87 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 88 through 154 )B88 - 154 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 155 through 212 )B155 - 212 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 213 through 239 )B213 - 239 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 240 through 276 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|