ソフトウェア | 名称 | バージョン | 分類 | NB |
---|
SCALEPACK | | データスケーリング | | PHASER | 2.1.4位相決定 | | PHENIX | 1.7.3_928精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | Blu-Ice | | データ収集 | | DENZO | | データ削減 | | | |
|
---|
精密化 | 構造決定の手法: 分子置換 / 解像度: 2.6→19.933 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 0 / 位相誤差: 24.2 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.2462 | 929 | 5.15 % | random |
---|
Rwork | 0.1833 | - | - | - |
---|
all | 0.1866 | 18030 | - | - |
---|
obs | 0.1866 | 18030 | 89.03 % | - |
---|
|
---|
溶媒の処理 | 減衰半径: 0.73 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 17.525 Å2 / ksol: 0.345 e/Å3 |
---|
原子変位パラメータ | Biso max: 109.47 Å2 / Biso mean: 37.5968 Å2 / Biso min: 2.04 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -4.6444 Å2 | 0 Å2 | -3.3332 Å2 |
---|
2- | - | -0.7115 Å2 | 0 Å2 |
---|
3- | - | - | -2.3168 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.6→19.933 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 5084 | 0 | 4 | 19 | 5107 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.009 | 5202 | X-RAY DIFFRACTION | f_angle_d1.162 | 7040 | X-RAY DIFFRACTION | f_chiral_restr0.076 | 758 | X-RAY DIFFRACTION | f_plane_restr0.005 | 930 | X-RAY DIFFRACTION | f_dihedral_angle_d15.539 | 1928 | | | | | |
|
---|
Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | タイプ | Rms dev position (Å) |
---|
1 | 1 | A2333 | X-RAY DIFFRACTION | POSITIONAL0.022 | 1 | 2 | B2333 | X-RAY DIFFRACTION | POSITIONAL0.022 | | | | |
|
---|
LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
---|
2.6-2.7368 | 0.2954 | 83 | 0.236 | 1520 | 1603 | 56 | 2.7368-2.9077 | 0.3694 | 106 | 0.2396 | 2089 | 2195 | 76 | 2.9077-3.1315 | 0.2918 | 141 | 0.2099 | 2543 | 2684 | 93 | 3.1315-3.4451 | 0.2734 | 146 | 0.1934 | 2747 | 2893 | 99 | 3.4451-3.9403 | 0.2105 | 143 | 0.159 | 2732 | 2875 | 100 | 3.9403-4.9518 | 0.1903 | 164 | 0.1459 | 2705 | 2869 | 99 | 4.9518-19.9334 | 0.2481 | 146 | 0.1905 | 2765 | 2911 | 99 |
|
---|
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 | 0.086 | 0.0112 | 0.0993 | 0.0738 | -0.0058 | 0.12 | 0.0233 | 0.1361 | 0.0361 | -0.0424 | -0.0192 | 0.0191 | -0.0243 | -0.0836 | 0.0043 | 0.0529 | 0.2091 | -0.0844 | 0.4926 | 0.0472 | 0.064 | 2.7096 | -23.9008 | 7.2787 | 2 | 0.1279 | 0.0823 | -0.0585 | 0.1919 | 0.0863 | 0.1431 | 0.0694 | 0.0201 | 0.1158 | -0.0396 | 0.0198 | 0.1252 | -0.1834 | -0.1231 | 0.0763 | 0.0365 | 0.2635 | -0.042 | -0.2189 | 0.0171 | 0.0733 | 24.5248 | -23.0927 | 19.613 | 3 | 0.043 | -0.0688 | -0.0564 | 0.1094 | 0.0902 | 0.074 | -0.0045 | -0.0274 | 0.0173 | 0.0384 | 0.0006 | 0.0226 | -0.0336 | -0.036 | 0.0055 | 0.14 | 0.0432 | 0.085 | 0.1249 | -0.1241 | 0.1859 | 17.994 | -20.2147 | 29.5596 | 4 | 0.0225 | -0.0063 | -0.0081 | 0.025 | 0.003 | 0.0028 | 0.0174 | -0.0277 | 0.0859 | 0.0076 | 0.0051 | -0.008 | -0.0598 | -0.025 | 0.0079 | 0.3917 | 0.2757 | 0.065 | 0.1892 | -0.1462 | 0.4357 | 11.6445 | -11.3154 | 19.3752 | 5 | 0.8167 | 0.2124 | -0.0937 | 0.3203 | 0.4782 | 0.9621 | -0.0338 | 0.1575 | 0.1745 | -0.0164 | -0.0704 | 0.0294 | -0.1853 | -0.2677 | -0.1758 | 0.0037 | 0.114 | -0.1018 | 0.1468 | 0.0615 | 0.1067 | 15.5582 | -24.2196 | 14.6923 | 6 | 0.0301 | 0.0106 | 0.0281 | 0.0271 | -0.0198 | 0.0646 | -0.0077 | -0.0382 | 0.0074 | 0.0279 | 0.0117 | 0.0111 | -0.0238 | -0.0222 | -0.0726 | 0.2029 | 0.0904 | 0.1502 | 0.3286 | -0.0429 | 0.1418 | 6.7052 | -22.1122 | 22.398 | 7 | 0.2676 | 0.0307 | 0.2626 | 0.0912 | 0.1628 | 0.5812 | -0.0762 | -0.0525 | 0.0971 | -0.0661 | -0.1022 | 0.045 | -0.1012 | -0.1594 | -0.5455 | 0.1222 | 0.169 | 0.0699 | 0.136 | -0.1075 | 0.0586 | 22.3709 | -29.7783 | 12.1043 | 8 | 0.0606 | -0.0165 | 0.0167 | 0.0042 | -0.0049 | 0.0045 | -0.0641 | 0.0939 | 0.0233 | -0.0022 | -0.0339 | -0.0289 | -0.0113 | 0.0197 | -0.0307 | 0.0697 | 0.0926 | 0.0107 | 0.4207 | -0.0373 | 0.3149 | 31.6037 | -45.8003 | 10.6873 | 9 | 0.0125 | -0.0289 | -0.0061 | 0.0612 | 0.0118 | 0.0267 | -0.0092 | 0.0293 | -0.05 | -0.0203 | 0.0029 | -0.0212 | 0.0429 | -0.0328 | 0.0925 | 0.0557 | -0.0392 | 0.2167 | 0.0161 | -0.1364 | -0.0726 | 18.7432 | -42.4731 | 7.8355 | 10 | 0.2331 | -0.0328 | 0.2524 | 0.2087 | 0.0607 | 0.3196 | -0.0026 | -0.1527 | -0.022 | 0.0734 | -0.0169 | 0.045 | 0.0272 | -0.1534 | 0.1141 | -0.1615 | -0.0119 | 0.1186 | 0.062 | 0.0498 | -0.1286 | 15.4808 | -32.723 | 10.9733 | 11 | 0.0152 | 0.01 | 0.026 | 0.0056 | 0.0158 | 0.0441 | -0.0185 | 0.0144 | -0.0108 | -0.0312 | -0.0047 | -0.0447 | 0.0121 | 0.0466 | -0.0513 | 0.0314 | -0.0072 | 0.0516 | 0.1651 | 0.0943 | 0.0453 | 35.1461 | -32.0428 | -0.0624 | 12 | 0.153 | -0.0712 | -0.2887 | 0.3551 | 0.2679 | 0.939 | 0.0078 | 0.0842 | -0.0142 | -0.0527 | -0.0833 | 0.0774 | 0.0619 | -0.2486 | -0.2044 | 0.1105 | 0.0637 | 0.0018 | 0.0806 | -0.1024 | -0.084 | 20.1709 | -36.873 | 0.8944 | 13 | 1.0051 | 0.1052 | 0.5665 | 0.2688 | 0.5192 | 1.1266 | -0.0918 | 0.3545 | 0.2297 | -0.1027 | -0.0074 | -0.0332 | -0.3519 | 0.0631 | -0.3528 | 0.0557 | 0.0349 | -0.1398 | 0.1465 | 0.344 | -0.4186 | 25.2959 | -24.4721 | -4.5647 | 14 | 0.2455 | 0.0525 | -0.1307 | 0.2312 | 0.1606 | 0.2445 | 0.0243 | -0.0105 | 0.0478 | 0.1567 | 0.0207 | -0.0613 | -0.062 | 0.0605 | 0.6667 | 0.2731 | 0.1038 | -0.1889 | 0.3103 | 0.1801 | 0.0505 | 25.6862 | -17.0409 | -0.591 | 15 | 0.0351 | -0.0233 | -0.0178 | 0.0158 | 0.0119 | 0.0091 | -0.0266 | 0.0089 | 0.0306 | -0.0166 | 0.0074 | -0.0314 | -0.0151 | 0.023 | 0.0083 | 0.741 | 0.025 | 0.0237 | 0.2698 | 0.2441 | 0.5571 | 28.8938 | -6.7627 | -0.9593 | 16 | 0.0112 | 0.0082 | 0.0031 | 0.0177 | 0.0344 | 0.0953 | 0.0114 | 0.0761 | 0.0478 | -0.0633 | 0.0165 | 0.0378 | -0.0798 | -0.0166 | 0.1984 | 0.4525 | 0.1363 | -0.2818 | 0.4043 | 0.2796 | 0.2716 | 18.3529 | -12.0298 | -9.042 | 17 | 0.3633 | -0.4683 | -0.1336 | 0.7961 | -0.061 | 0.3248 | -0.0468 | 0.0029 | 0.2048 | -0.0697 | 0.0237 | -0.2156 | -0.3003 | 0.0312 | 0.1851 | 0.3474 | 0.0976 | -0.0866 | -0.0574 | -0.0216 | 0.1165 | 28.3191 | -14.6789 | 18.1206 | 18 | 0.0425 | -0.0705 | 0.002 | 0.1109 | -0.0086 | 0.0315 | 0.0236 | 0.0162 | 0.0982 | -0.0039 | 0.0419 | 0.0949 | -0.084 | -0.0185 | 0.1159 | 0.6408 | 0.1547 | -0.0096 | 0.0429 | 0.0387 | 0.5496 | 22.4775 | -5.3908 | 9.3845 | 19 | 0.002 | -0.0024 | -0.001 | 0.0046 | -0.0023 | 0.0059 | 0.0049 | -0.0149 | 0.0093 | -0.0392 | -0.017 | 0.0188 | -0.0168 | -0.0754 | -0.0001 | 0.824 | 0.1781 | 0.0467 | 0.5218 | 0.2902 | 0.6302 | 13.4787 | -1.2278 | -5.4286 | 20 | 0.8958 | -0.1563 | 0.5852 | 0.1462 | -0.1268 | 0.5144 | -0.1013 | 0.124 | 0.2585 | -0.0062 | -0.0495 | -0.0679 | -0.1315 | -0.0254 | -0.157 | 0.1677 | 0.2542 | -0.0553 | 0.4909 | 0.1574 | 0.1889 | 9.3665 | -15.9269 | -1.8728 | 21 | 0.0581 | 0.0543 | -0.0071 | 0.0772 | -0.0094 | 0.0016 | 0.0132 | -0.0937 | -0.0368 | 0.0275 | -0.0001 | -0.0139 | 0.0317 | 0.067 | 0.3534 | 0.0737 | -0.0142 | -0.0625 | 0.5592 | 0.2539 | 0.0824 | 39.4368 | -42.885 | 47.7403 | 22 | 0.2151 | 0.3064 | -0.0825 | 0.5762 | 0.0624 | 0.2555 | -0.076 | -0.1208 | -0.2352 | 0.1881 | -0.1205 | -0.1406 | 0.1711 | 0.0548 | -0.6563 | 0.1218 | 0.0588 | 0.0303 | -0.221 | 0.2557 | -0.0246 | 29.2183 | -43.6899 | 24.8445 | 23 | 0.0313 | 0.0507 | -0.0158 | 0.093 | -0.0342 | 0.0143 | -0.0124 | 0.0009 | -0.0341 | 0.0086 | 0.0101 | 0.0419 | 0.0222 | -0.0178 | 0.0222 | 0.35 | -0.1854 | 0.0004 | 0.2725 | 0.0979 | 0.2819 | 18.6995 | -46.5657 | 30.4187 | 24 | 0.003 | 0.0087 | -0.001 | 0.0283 | 0.01 | 0.0235 | 0.0032 | -0.0378 | -0.0675 | 0.0138 | -0.0118 | -0.0249 | 0.093 | -0.018 | 0.0318 | 0.305 | -0.1223 | 0.0979 | 0.1495 | 0.2648 | 0.3174 | 28.235 | -55.4656 | 37.7021 | 25 | 0.8614 | 0.3537 | -0.2856 | 0.2695 | 0.0862 | 0.4202 | 0.0411 | -0.2263 | -0.1976 | 0.0361 | -0.0585 | -0.0452 | 0.1523 | 0.1262 | -0.2163 | 0.0735 | 0.0996 | -0.1012 | 0.0963 | 0.1105 | 0.0029 | 33.2698 | -42.5628 | 34.2458 | 26 | 0.3162 | -0.0308 | -0.1426 | 0.0175 | 0.0729 | 0.2975 | -0.0374 | -0.0237 | -0.0568 | 0.0053 | 0.0018 | 0.0112 | 0.062 | -0.0312 | -0.0298 | 0.0426 | -0.0324 | 0.0765 | 0.3452 | 0.0974 | 0.0613 | 24.7622 | -44.6665 | 42.3379 | 27 | 0.1622 | 0.0299 | -0.0896 | 0.3146 | -0.0214 | 0.1145 | 0.0772 | -0.1092 | -0.0713 | -0.0875 | -0.0341 | -0.0387 | 0.0342 | 0.0092 | 0.357 | 0.0769 | -0.0945 | 0.1942 | 0.1222 | 0.1306 | 0.0507 | 36.4871 | -37.0338 | 27.7192 | 28 | 0.0081 | -0.0108 | -0.0206 | 0.0541 | -0.0284 | 0.1256 | 0.0028 | 0.0009 | -0.0031 | -0.0336 | 0.0064 | 0.0074 | 0.0457 | 0.0844 | 0.0532 | 0.2911 | -0.1138 | 0.0318 | 0.4252 | 0.105 | 0.14 | 38.7673 | -20.9824 | 18.6433 | 29 | 0.0984 | -0.0008 | -0.0111 | 0.0353 | 0.0165 | 0.0096 | 0.0585 | -0.0519 | 0.0808 | -0.0445 | 0.0084 | -0.0514 | -0.1034 | 0.0438 | -0.032 | 0.0658 | -0.1278 | 0.1979 | 0.0971 | -0.0821 | 0.0985 | 40.3962 | -24.3149 | 31.7205 | 30 | 0.2337 | 0.0374 | 0.241 | 0.1258 | 0.0536 | 0.3023 | 0.0223 | -0.1562 | 0.0205 | 0.0338 | -0.0287 | 0.0757 | 0.0089 | -0.2085 | -0.0409 | -0.0816 | -0.0002 | 0.1155 | 0.1327 | -0.0105 | -0.127 | 36.9601 | -34.0671 | 34.6839 | 31 | 0.1099 | 0.0846 | 0.0048 | 0.1677 | 0.0289 | 0.0061 | -0.0163 | 0.044 | -0.0199 | -0.0359 | 0.0306 | -0.034 | -0.0106 | 0.0092 | -0.0048 | 0.0868 | 0.0671 | 0.0321 | 0.1316 | 0.0132 | 0.0754 | 49.7937 | -34.7441 | 16.1292 | 32 | 0.6461 | 0.0124 | -0.102 | 0.1328 | -0.0082 | 0.0922 | 0.0571 | -0.2337 | 0.0238 | 0.1137 | -0.0634 | -0.1409 | -0.0007 | 0.0647 | 0.1114 | -0.1012 | -0.1709 | -0.177 | 0.0285 | -0.0317 | 0.024 | 47.4322 | -29.91 | 30.9516 | 33 | 0.369 | 0.183 | 0.3583 | 0.1084 | 0.0979 | 0.584 | 0.0938 | -0.0121 | -0.3345 | -0.0241 | -0.0017 | -0.1238 | 0.2415 | 0.2762 | -0.6612 | -0.4623 | 0.2309 | -0.3517 | 0.2024 | 0.0344 | 0.0122 | 53.3473 | -42.3108 | 26.359 | 34 | 0.1151 | 0.1401 | -0.0578 | 0.2944 | 0.0939 | 0.2953 | -0.0208 | 0.1129 | -0.0641 | -0.1019 | -0.0786 | 0.1379 | 0.0469 | -0.0042 | -0.7961 | 0.0472 | 0.1886 | -0.2139 | 0.3652 | 0.1315 | 0.3426 | 49.4542 | -49.7409 | 25.579 | 35 | 0.0173 | 0.0182 | -0.0185 | 0.0192 | -0.0193 | 0.0197 | 0.0136 | 0.0209 | -0.0282 | -0.0076 | 0.0133 | -0.0592 | 0.0285 | 0.0142 | -0.0028 | 0.4591 | 0.1949 | 0.0426 | 0.184 | 0.0913 | 0.6628 | 50.1025 | -60.0219 | 22.4397 | 36 | 0.0446 | 0.0066 | -0.0321 | 0.0011 | -0.005 | 0.026 | 0.0282 | 0.0123 | -0.0802 | -0.0005 | -0.0212 | -0.0492 | 0.0483 | 0.065 | -0.0731 | 0.252 | 0.2646 | -0.2793 | 0.4057 | 0.175 | 0.4898 | 57.1557 | -54.7554 | 33.6981 | 37 | 0.1003 | -0.177 | 0.0629 | 0.7153 | -0.5198 | 0.4682 | 0.0029 | -0.003 | -0.2103 | -0.1913 | -0.0352 | -0.0964 | 0.191 | 0.048 | -0.2756 | 0.0955 | 0.0217 | -0.1017 | -0.0265 | 0.1589 | 0.3447 | 31.1297 | -52.1614 | 21.2748 | 38 | 0.039 | -0.0508 | 0.0306 | 0.0812 | -0.0543 | 0.0357 | -0.0478 | -0.0088 | -0.0878 | 0.1138 | 0.0341 | 0.0724 | 0.1477 | 0.0081 | -0.0396 | 0.4991 | 0.062 | -0.0353 | 0.1187 | 0.1959 | 0.7111 | 39.1545 | -61.4009 | 27.8719 | 39 | 0.0805 | 0.0873 | -0.0272 | 0.1014 | -0.0186 | 0.0291 | -0.0229 | -0.0389 | 0.0145 | 0.034 | 0.0219 | 0.0057 | 0.0002 | -0.0115 | -0.0058 | 0.5736 | 0.2662 | -0.0193 | 0.4457 | 0.1872 | 0.8415 | 53.1026 | -65.5526 | 38.2125 | 40 | 0.0623 | -0.0158 | 0.1192 | 0.1064 | -0.0418 | 0.3622 | 0.1281 | -0.0428 | -0.1009 | 0.0099 | -0.0043 | -0.0038 | 0.2847 | 0.0647 | 0.0401 | 0.1837 | 0.0935 | -0.0609 | 0.4103 | 0.2523 | 0.1611 | 49.1709 | -50.8549 | 41.9692 |
|
---|
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 3:19)A3 - 19 | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 20:41)A20 - 41 | 3 | X-RAY DIFFRACTION | 3 | (chain A and resid 42:47)A42 - 47 | 4 | X-RAY DIFFRACTION | 4 | (chain A and resid 48:61)A48 - 61 | 5 | X-RAY DIFFRACTION | 5 | (chain A and resid 62:81)A62 - 81 | 6 | X-RAY DIFFRACTION | 6 | (chain A and resid 82:87)A82 - 87 | 7 | X-RAY DIFFRACTION | 7 | (chain A and resid 88:109)A88 - 109 | 8 | X-RAY DIFFRACTION | 8 | (chain A and resid 110:114)A110 - 114 | 9 | X-RAY DIFFRACTION | 9 | (chain A and resid 115:131)A115 - 131 | 10 | X-RAY DIFFRACTION | 10 | (chain A and resid 132:149)A132 - 149 | 11 | X-RAY DIFFRACTION | 11 | (chain A and resid 150:155)A150 - 155 | 12 | X-RAY DIFFRACTION | 12 | (chain A and resid 156:175)A156 - 175 | 13 | X-RAY DIFFRACTION | 13 | (chain A and resid 176:217)A176 - 217 | 14 | X-RAY DIFFRACTION | 14 | (chain A and resid 218:240)A218 - 240 | 15 | X-RAY DIFFRACTION | 15 | (chain A and | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|