ソフトウェア | 名称 | バージョン | 分類 |
---|
Blu-Ice | iceデータ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.7.3_928)精密化 | d*TREK | | データ削減 | d*TREK | | データスケーリング | PHENIX | | 位相決定 | | |
|
---|
精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.5→46.185 Å / SU ML: 0.26 / σ(F): 1.34 / 位相誤差: 22.61 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.2288 | 1134 | 5.11 % |
---|
Rwork | 0.1822 | - | - |
---|
obs | 0.1845 | 22208 | 99.95 % |
---|
all | - | 22208 | - |
---|
|
---|
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 | | Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 2.9055 Å2 | 0 Å2 | -0 Å2 |
---|
2- | - | 2.9055 Å2 | -0 Å2 |
---|
3- | - | - | -5.8111 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.5→46.185 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 2626 | 0 | 48 | 142 | 2816 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.004 | 2720 | X-RAY DIFFRACTION | f_angle_d0.878 | 3652 | X-RAY DIFFRACTION | f_dihedral_angle_d15.538 | 999 | X-RAY DIFFRACTION | f_chiral_restr0.074 | 389 | X-RAY DIFFRACTION | f_plane_restr0.002 | 469 | | | | | |
|
---|
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 (%) |
---|
2.5001-2.6139 | 0.3206 | 125 | 0.2543 | 2586 | X-RAY DIFFRACTION | 100 | 2.6139-2.7517 | 0.2833 | 168 | 0.2282 | 2559 | X-RAY DIFFRACTION | 100 | 2.7517-2.9241 | 0.2611 | 154 | 0.2061 | 2574 | X-RAY DIFFRACTION | 100 | 2.9241-3.1498 | 0.2811 | 157 | 0.2097 | 2579 | X-RAY DIFFRACTION | 100 | 3.1498-3.4667 | 0.2618 | 130 | 0.191 | 2644 | X-RAY DIFFRACTION | 100 | 3.4667-3.9681 | 0.2058 | 128 | 0.1641 | 2630 | X-RAY DIFFRACTION | 100 | 3.9681-4.9984 | 0.1656 | 128 | 0.1425 | 2677 | X-RAY DIFFRACTION | 100 | 4.9984-46.193 | 0.2363 | 144 | 0.1931 | 2825 | X-RAY DIFFRACTION | 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 | 2.4211 | 0.1844 | -0.5642 | 2.2503 | -6.9002 | 2.1396 | -0.725 | 0.7781 | 0.2501 | -0.5867 | -0.4641 | -0.8419 | -1.1869 | 1.0302 | 1.258 | 0.6787 | -0.1844 | -0.088 | 0.5306 | -0.0544 | 0.5287 | 31.2339 | 75.7892 | 76.4529 | 2 | 2.1267 | 2.0765 | 6.2776 | 1.9573 | 2.088 | 2.0562 | -0.0926 | 0.6126 | 0.7296 | 0.2044 | 0.5224 | -0.677 | -1.221 | 0.2087 | -0.3694 | 0.6731 | 0.1401 | -0.0834 | 0.5171 | -0.0553 | 0.6243 | 34.9322 | 75.1928 | 92.5234 | 3 | 6.9477 | -0.7319 | -2.8275 | 0.3452 | -0.0094 | 1.4675 | 0.0642 | 1.8325 | 0.4876 | 0.5336 | -0.5451 | -0.9994 | 1.1793 | -0.8244 | -0.044 | 1.1828 | -0.3535 | -0.1142 | 0.9158 | -0.0046 | 1.0844 | 46.2109 | 77.1931 | 86.6136 | 4 | 2.0609 | 5.6923 | -2.5234 | 5.3593 | 0.1451 | 1.1692 | 0.4863 | -1.3961 | 1.024 | 0.5893 | -0.3289 | -0.6626 | -1.6228 | 0.9423 | 0.0118 | 0.8327 | -0.3431 | -0.0757 | 1.4622 | -0.2194 | 1.0081 | 56.5934 | 66.7399 | 85.1138 | 5 | 2.0579 | -4.018 | 0.1107 | 2.0279 | 5.4216 | 1.208 | -0.1734 | -0.3331 | 0.0776 | 1.911 | -0.3917 | -1.6377 | 0.9749 | 1.1276 | 0.3544 | 0.7737 | 0.1404 | -0.1068 | 1.2433 | -0.1841 | 0.9577 | 50.7674 | 58.6293 | 86.4667 | 6 | 2.7117 | 2.3709 | 5.4199 | 7.3052 | 5.5508 | 5.8598 | -0.8264 | 1.458 | -0.3808 | -0.9109 | 1.7606 | -1.907 | -0.4396 | 2.7095 | -0.8747 | 0.738 | -0.1158 | -0.0177 | 1.4052 | -0.3147 | 0.8815 | 53.8582 | 58.3089 | 76.0165 | 7 | 0.3765 | -1.0524 | -0.8632 | 7.9565 | 4.6964 | 2.5018 | -0.3189 | -0.2258 | 0.0286 | 0.9003 | -0.0376 | 0.2223 | 1.0946 | -0.4619 | 0.4186 | 0.8109 | 0.1989 | -0.0848 | 1.0036 | -0.2501 | 0.5772 | 44.4531 | 38.4087 | 77.4859 | 8 | 2.8306 | -1.0421 | -7.0993 | 2.6068 | -0.1918 | 2.2847 | -0.0445 | -0.5019 | -0.4036 | 0.7052 | -0.0872 | -0.0472 | 0.7534 | 0.831 | 0.1724 | 0.4979 | -0.0586 | 0.0043 | 0.4963 | 0.0405 | 0.4496 | 53.9063 | 20.7897 | 64.512 | 9 | 5.7434 | -1.1196 | -3.6172 | 6.7251 | 1.5314 | 6.9319 | -0.0227 | 0.4352 | -0.3556 | -0.4218 | -0.138 | -0.2808 | 0.6635 | -0.045 | 0.1725 | 0.3578 | -0.0008 | 0.0055 | 0.283 | -0.0318 | 0.2928 | 57.0926 | 13.8651 | 44.344 | 10 | 4.8948 | 0.311 | -1.0393 | 6.3167 | -0.7147 | 2.9218 | -0.2344 | 0.7341 | -0.3968 | -0.7279 | 0.0137 | 0.2262 | 0.7835 | -0.8625 | 0.2798 | 0.3729 | -0.0673 | 0.027 | 0.4585 | -0.0746 | 0.3548 | 47.6442 | 15.3998 | 44.0249 | 11 | 2.8668 | -6.1337 | 2.3697 | 2.6422 | -8.0521 | 2.4774 | -0.4798 | -1.0482 | 0.0104 | 1.1704 | 0.8173 | 0.3309 | -0.9122 | -1.3626 | -0.7252 | 0.5748 | -0.0115 | 0.0099 | 0.7855 | -0.0729 | 0.6787 | 40.5355 | 22.8796 | 54.8256 | 12 | 7.4411 | 1.4666 | -4.4394 | 8.9794 | -3.5266 | 4.3692 | -0.0811 | 0.9449 | 0.2514 | -0.8768 | 0.2292 | 0.1508 | 0.1149 | -0.2966 | -0.1575 | 0.3686 | 0.0211 | -0.0215 | 0.5539 | 0.0441 | 0.3041 | 48.9011 | 31.2773 | 39.5225 | 13 | 6.5963 | 2.4915 | -7.1773 | 5.0441 | -2.7349 | 2.9131 | 0.1503 | 0.0372 | 0.3196 | -0.0002 | 0.1644 | 0.3819 | -0.1054 | -0.392 | -0.3291 | 0.2087 | 0.0036 | 0.0005 | 0.4293 | 0.0275 | 0.2591 | 48.2281 | 27.7579 | 52.7362 | 14 | 3.1658 | -8.1317 | -1.6304 | 9.756 | 5.4285 | 6.9887 | 0.304 | -0.1029 | 0.2347 | -0.5346 | -0.2617 | -0.1179 | -0.9286 | 0.4947 | -0.048 | 0.4288 | 0.0015 | 0.0768 | 0.3632 | 0.065 | 0.4098 | 58.6911 | 37.9396 | 41.211 | 15 | 3.2912 | -0.3014 | -1.6908 | 3.7652 | -1.0696 | 6.1731 | 0.358 | 0.0549 | 0.4076 | 0.5428 | -0.2683 | 0.1555 | -0.7218 | -0.5275 | -0.0894 | 0.3734 | -0.0007 | 0.0296 | 0.2915 | -0.0303 | 0.3283 | 52.113 | 34.6099 | 53.3863 | 16 | 2.1857 | 3.2019 | -3.153 | 2.1461 | 0.3969 | 2.1688 | 2.138 | 0.3607 | 2.2215 | -1.0016 | -0.3718 | -0.2733 | -3.3604 | -0.1212 | -1.6073 | 0.9697 | -0.1044 | 0.1814 | 0.6312 | 0.1058 | 0.601 | 63.265 | 41.1689 | 48.8979 | 17 | 2.3735 | -6.336 | -0.9778 | 9.3331 | -1.6714 | 2.3453 | 0.0036 | -0.9014 | 1.3609 | 1.0236 | 0.2064 | -0.5325 | -1.0999 | 0.5002 | -0.3112 | 0.5427 | -0.0474 | 0.0771 | 0.4894 | -0.0592 | 0.5332 | 60.0557 | 35.1846 | 58.4235 | 18 | 6.0966 | -1.8531 | -4.5062 | 7.9401 | 4.3094 | 2.9657 | -0.0346 | -0.6089 | 0.2692 | 0.1451 | 0.1701 | -0.3492 | 0.0377 | 1.0135 | -0.3254 | 0.3437 | -0.0364 | 0.0092 | 0.384 | 0.0084 | 0.3427 | 71.222 | 23.3314 | 48.6547 | 19 | 5.1819 | -2.8219 | -5.0991 | 4.032 | 1.864 | 7.6857 | 0.3857 | 0.518 | 0.0036 | -0.2494 | -0.4251 | -0.3695 | -0.2046 | -0.4168 | 0.2896 | 0.3535 | -0.0226 | -0.0037 | 0.3661 | 0.0091 | 0.3392 | 66.1899 | 28.0899 | 47.6259 | 20 | 6.4369 | -4.623 | -5.4788 | 6.7545 | 5.4766 | 4.4253 | -0.2361 | -0.3828 | -0.1816 | 0.2404 | 0.3193 | -0.0526 | 0.7045 | 0.4539 | -0.0178 | 0.3459 | 0.0117 | 0.0223 | 0.2949 | 0.0306 | 0.3097 | 64.3228 | 16.978 | 52.2645 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
---|
1 | X-RAY DIFFRACTION | 1 | (chain A and resid 21:27)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 28:34)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 35:41)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 42:52)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 53:61)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 62:89)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 90:114)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 115:123)9 | X-RAY DIFFRACTION | 9 | (chain A and resid 124:161)10 | X-RAY DIFFRACTION | 10 | (chain A and resid 162:193)11 | X-RAY DIFFRACTION | 11 | (chain A and resid 194:201)12 | X-RAY DIFFRACTION | 12 | (chain A and resid 202:217)13 | X-RAY DIFFRACTION | 13 | (chain A and resid 218:235)14 | X-RAY DIFFRACTION | 14 | (chain A and resid 236:251)15 | X-RAY DIFFRACTION | 15 | (chain A and resid 252:276)16 | X-RAY DIFFRACTION | 16 | (chain A and resid 277:281)17 | X-RAY DIFFRACTION | 17 | (chain A and resid 282:290)18 | X-RAY DIFFRACTION | 18 | (chain A and | | | | | | | | | | | | | | | | | |
|
---|