Software Name Version Classification XSCALEdata scaling MOLREPphasing PHENIX(dev_2443: ???)refinement PDB_EXTRACT3.2 data extraction XDSdata scaling Cootmodel building
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 5GHWResolution : 1.6→49.072 Å / SU ML : 0.15 / Cross valid method : FREE R-VALUE / σ(F) : 1.34 / Phase error : 18.78 Rfactor Num. reflection % reflection Rfree 0.1919 1931 1.76 % Rwork 0.1647 - - obs 0.1652 109637 99.29 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 ÅDisplacement parameters Biso max : 86.15 Å2 / Biso mean : 30.2831 Å2 / Biso min : 13.22 Å2 Refinement step Cycle : final / Resolution : 1.6→49.072 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 5137 0 88 684 5909 Biso mean - - 52.14 38.74 - Num. residues - - - - 659
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.006 5528 X-RAY DIFFRACTION f_angle_d0.873 7510 X-RAY DIFFRACTION f_chiral_restr0.061 816 X-RAY DIFFRACTION f_plane_restr0.007 994 X-RAY DIFFRACTION f_dihedral_angle_d13.451 3327
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 14
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.6-1.64 0.2557 134 0.2284 7628 7762 100 1.64-1.6844 0.2206 142 0.2065 7607 7749 100 1.6844-1.7339 0.2156 164 0.1911 7666 7830 100 1.7339-1.7899 0.2046 124 0.1796 7658 7782 100 1.7899-1.8539 0.2064 127 0.1751 7695 7822 100 1.8539-1.9281 0.2241 145 0.1765 7706 7851 100 1.9281-2.0159 0.2424 147 0.1714 7629 7776 100 2.0159-2.1221 0.1819 149 0.1678 7711 7860 100 2.1221-2.2551 0.1935 141 0.1679 7700 7841 100 2.2551-2.4292 0.194 114 0.168 7727 7841 99 2.4292-2.6737 0.212 125 0.1743 7690 7815 99 2.6737-3.0605 0.2213 135 0.1749 7723 7858 99 3.0605-3.8557 0.1684 143 0.1544 7747 7890 98 3.8557-49.0949 0.165 141 0.1433 7819 7960 96
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 38) Hide large table 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 6.2293 -1.9185 -5.2879 3.0825 4.1929 9.1066 -0.1529 -0.1867 0.1617 0.5107 -0.0154 0.5303 -0.6364 -0.5863 0.1392 0.372 0.0633 0.0629 0.2114 -0.0123 0.2488 -24.0323 10.6157 3.3673 2 7.6279 2.8622 -5.2235 4.1348 -3.1268 3.9813 -0.2146 -0.4809 -0.3359 0.1023 -0.1887 -0.0775 0.3052 0.2052 0.5319 0.2233 -0.0052 0.0162 0.1596 -0.0006 0.1181 -19.1866 -4.3261 11.3031 3 4.1267 -1.9266 2.5584 5.6486 -4.5501 3.9819 -0.1008 -0.152 0.1987 0.4113 0.1137 0.2241 -0.5137 -0.716 -0.024 0.2195 0.0232 0.0663 0.2774 -0.0297 0.2068 -31.9231 2.6317 11.1215 4 1.2446 0.2389 -0.4586 2.4366 -0.26 2.1361 -0.0455 0.217 -0.024 -0.1024 -0.0363 0.4051 0.2456 -0.5811 0.0679 0.1841 -0.0419 0.0167 0.2714 -0.0286 0.1814 -31.0492 -3.2544 -0.2949 5 2.8994 -0.6019 0.2393 4.2901 -3.5158 4.0964 -0.0781 0.346 -0.402 -0.3036 -0.2386 0.0055 0.9367 -0.1598 0.1794 0.3151 -0.0615 0.0578 0.1939 -0.0318 0.1987 -25.9175 -11.135 -14.7655 6 1.7855 1.1094 -0.1374 3.6549 -0.2566 3.589 0.0165 0.0392 0.0298 0.0802 -0.0069 0.1161 0.1541 -0.3387 0.0084 0.0991 -0.008 0.017 0.1402 -0.0009 0.1134 -26.3107 1.2136 -10.9545 7 0.6524 -0.0267 0.2987 0.9 -1.8262 3.8462 0.052 0.0231 -0.1092 0.3911 -0.0382 0.2935 1.4828 -0.5964 0.0779 0.4073 -0.1471 0.0748 0.2197 -0.0115 0.2582 -28.77 -14.0774 5.1517 8 2.3675 0.038 0.1266 1.2098 -0.9498 3.2764 -0.061 -0.0269 -0.1469 0.0902 0.013 0.1853 0.3381 -0.3877 0.0064 0.2338 -0.0393 0.0623 0.1342 -0.015 0.1581 -27.8602 -9.396 -2.837 9 2.6648 1.0479 2.3695 3.8185 -0.4869 2.7505 0.1068 0.2228 -0.0909 0.1401 0.0427 -0.0679 0.395 0.7295 -0.1301 0.1987 0.0281 0.0097 0.2062 -0.007 0.1529 -18.7455 -0.5145 -12.1284 10 4.3631 -0.1114 0.2523 6.3277 1.2876 8.6937 -0.0195 0.1442 0.2846 -0.1086 0.0736 0.5913 -0.2565 -0.5649 -0.0661 0.1265 -0.0097 0.0003 0.21 0.0408 0.2051 -28.8475 6.727 -19.4195 11 6.7662 2.4858 -3.0946 5.9968 -2.2798 6.2043 0.1187 -0.4446 -0.3418 0.1167 -0.2516 0.0782 0.2483 -0.3022 0.1295 0.1526 -0.0326 -0.0021 0.2429 0.0112 0.1732 -26.7124 -5.426 -34.7152 12 2.4873 -1.2631 0.8928 5.4478 -1.5061 1.5599 -0.1787 -0.4878 -0.0664 0.5779 0.0882 -0.1372 0.0081 0.0662 0.1222 0.2436 0.0162 0.0066 0.2874 0.0114 0.1138 -12.7607 -4.2014 -22.7672 13 6.4325 0.8476 4.466 3.6372 2.4942 7.1289 0.2569 -0.4096 -0.7471 -0.1459 0.2531 0.4719 1.2733 -0.5835 -0.4164 0.4748 -0.061 -0.0318 0.2069 0.1182 0.3427 -20.3152 -16.4088 -26.4969 14 4.5339 -0.8353 -0.3482 5.0019 1.0782 3.6426 0.0377 0.2699 -0.7622 -0.2628 -0.0291 -0.0229 0.6622 -0.0095 0.0432 0.2842 0.0181 0.0071 0.1573 -0.0249 0.1983 -15.5806 -13.8396 -34.0158 15 4.7389 -0.0007 -0.8275 2.577 0.4991 2.8124 0.029 -0.1849 -0.0167 0.2223 0.0324 -0.1048 0.2093 0.231 -0.0665 0.2258 0.0764 -0.0063 0.2296 -0.0047 0.1467 -5.5137 -8.6157 -32.5079 16 9.7712 0.5904 -0.0624 0.7326 -0.313 1.0475 -0.0532 0.2987 -0.1183 -0.0636 0.0216 -0.0685 0.2516 0.1797 0.0543 0.2428 0.048 0.0001 0.1732 -0.0078 0.1527 -12.8818 -9.0943 -48.4932 17 4.6679 1.8069 -5.7725 1.6581 -2.7378 8.1407 0.0202 -0.6814 -0.2423 0.1959 -0.0667 0.0615 0.1075 1.184 0.1528 0.2808 0.1611 -0.0024 0.2753 0.0349 0.1947 -3.8074 -12.5353 -30.5652 18 2.2016 -0.3018 0.9092 0.8763 0.2168 3.6978 -0.1228 -0.1079 -0.1688 0.0337 0.0621 0.0178 0.1032 0.2141 0.0598 0.1415 0.0274 0.0129 0.1742 0.0071 0.1244 -10.4175 -8.3363 -41.5358 19 9.5763 3.1569 -3.0231 6.216 -1.5358 6.0962 -0.078 0.3722 -0.6092 -0.1142 0.194 0.154 0.823 -0.2261 -0.1468 0.2856 0.0123 -0.0641 0.1705 -0.0274 0.1975 -23.3839 -11.1395 -55.9815 20 3.7165 -1.5911 1.0641 4.9875 0.0647 7.3616 -0.1136 0.4558 0.5166 -0.3353 0.2824 0.2482 -0.4103 -0.5451 -0.1453 0.1254 -0.0142 -0.0254 0.2795 0.1053 0.2966 -27.1011 15.1711 -26.7223 21 1.9167 0.6719 -1.4324 2.1768 -1.8496 2.3522 -0.1393 0.4063 0.4058 -0.5523 0.3621 0.4103 -0.4704 -0.14 -0.2021 0.3306 -0.09 -0.0541 0.28 0.1081 0.2756 -19.2225 23.8683 -32.8836 22 7.1855 3.2851 -5.5623 6.1889 -3.1885 6.4879 0.2017 -0.4779 0.0745 0.4673 -0.2027 0.1132 -0.6149 0.6558 -0.0429 0.3222 -0.1331 0.0308 0.2326 -0.0158 0.2277 -10.5188 26.5223 -17.2302 23 4.241 2.3331 2.3115 3.6171 -1.5227 5.0305 -0.2391 0.5875 0.0327 -0.6239 0.2883 0.0664 -0.1908 0.6095 0.009 0.2233 -0.1585 0.039 0.3318 -0.0047 0.1565 -8.1183 20.6128 -34.1517 24 9.3777 -1.5026 -6.0782 1.7963 0.85 3.9764 -0.1256 -0.3379 -0.2404 0.0758 0.1766 -0.5608 0.2849 1.1016 0.0042 0.1652 0.0395 0.0163 0.4946 -0.0278 0.3472 -1.9744 12.297 -19.8249 25 1.8059 1.1968 -0.7604 2.0267 -0.8914 2.3701 -0.0391 0.2102 0.0586 -0.3375 0.2038 -0.1242 -0.2366 0.4209 -0.1259 0.2059 -0.0686 0.0283 0.2624 -0.0174 0.1869 -10.0697 18.6969 -27.0243 26 3.0866 1.5066 -1.459 2.6288 0.0546 2.0494 -0.0654 0.0839 -0.0359 -0.1278 0.1533 -0.1782 -0.1791 0.5178 -0.0024 0.1253 -0.0497 0.0045 0.251 -0.0028 0.1566 -9.8958 14.6935 -24.8771 27 7.3647 2.9868 2.8004 3.5435 5.5065 9.3895 -0.1482 -0.3263 0.6659 0.0241 0.2831 0.2063 -0.8114 0.3155 -0.1477 0.2989 -0.0284 0.0368 0.1764 -0.0134 0.2276 -16.919 17.2553 -6.8271 28 6.819 2.4829 0.067 4.5391 1.8677 4.9409 0.1027 0.2515 -0.0775 -0.2673 0.0203 0.4743 0.6288 -0.348 -0.1174 0.2607 -0.025 -0.0838 0.1441 0.0027 0.2294 -31.3702 -8.7585 -63.3308 29 4.4563 -0.6325 2.7413 1.7008 -0.7348 2.5324 0.4612 0.9965 -0.2916 -0.4551 -0.1716 0.2071 0.5539 0.1008 -0.2354 0.3519 0.0353 -0.0899 0.4266 -0.0329 0.208 -33.2202 -0.3335 -78.5423 30 4.4461 -0.7985 3.0279 3.0109 -1.8136 7.9221 0.1362 -0.2409 -0.6752 -0.321 0.3874 0.9929 0.6574 -1.1281 -0.3651 0.3001 -0.1088 -0.1664 0.47 0.0891 0.5637 -44.6529 -3.1963 -70.5676 31 5.664 -0.1461 0.7054 5.4039 -2.8763 8.2936 0.1764 -0.0678 -0.0917 0.0914 0.185 0.414 0.1614 -0.337 -0.2374 0.2274 -0.0196 -0.0713 0.1618 0.0116 0.2239 -36.1178 -2.1654 -67.0481 32 2.2687 -2.981 -3.0788 4.0701 3.8461 4.5037 -0.0297 -0.1897 -0.1715 0.1234 -0.1242 0.7884 0.3296 -1.1108 0.1751 0.179 0.0369 -0.0264 0.4544 0.0045 0.341 -41.9345 7.4167 -65.6774 33 3.6787 -0.4649 -0.1731 3.1629 0.0552 4.5466 -0.0086 0.2687 0.2512 -0.1099 0.0678 0.0014 -0.3589 -0.0791 -0.0303 0.1996 0.0463 -0.0343 0.2266 0.0253 0.2251 -33.4854 10.5718 -71.5791 34 7.6598 4.644 -4.0989 4.6061 -0.5977 4.2642 0.3108 -0.3172 0.4876 0.2677 -0.2176 0.2225 -0.9204 0.5643 -0.0368 0.3716 -0.0368 -0.0628 0.2331 -0.0268 0.2852 -27.3921 15.4428 -55.3984 35 1.8907 -0.0737 -0.0814 6.4154 -3.1797 6.7617 -0.0505 -0.0903 0.0657 0.005 -0.0188 0.1377 -0.1221 -0.2432 0.0457 0.119 0.0194 -0.0295 0.1782 -0.0227 0.1688 -30.6452 3.2913 -54.0867 36 3.9605 1.6335 1.817 5.811 3.9275 7.141 -0.2048 0.4468 0.4223 -0.4514 0.1553 0.4195 -0.7472 -0.2663 0.0403 0.3192 0.0788 -0.0805 0.2401 0.0774 0.2928 -37.2347 13.0971 -73.0975 37 2.1482 -0.7027 0.9092 2.9692 -1.4195 4.8557 -0.0144 -0.0399 0.1692 0.0435 0.0703 0.1655 -0.3475 -0.3018 -0.0664 0.1656 0.0102 -0.0306 0.1405 -0.0071 0.1783 -30.885 8.7419 -62.0551 38 2.4122 2.0002 -3.2122 9.7867 0.1746 5.5535 0.3119 -0.305 0.0881 0.6052 -0.1226 0.5607 -0.3312 -0.6402 -0.1988 0.2391 0.0459 -0.0103 0.3375 0.0078 0.2118 -30.4124 1.0081 -43.9072
Refinement TLS group Show large table (6 x 38) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 0 through 13 )A0 - 13 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 14 through 25 )A14 - 25 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 26 through 41 )A26 - 41 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 42 through 87 )A42 - 87 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 88 through 97 )A88 - 97 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 98 through 112 )A98 - 112 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 113 through 125 )A113 - 125 8 X-RAY DIFFRACTION 8 chain 'A' and (resid 126 through 147 )A126 - 147 9 X-RAY DIFFRACTION 9 chain 'A' and (resid 148 through 157 )A148 - 157 10 X-RAY DIFFRACTION 10 chain 'A' and (resid 158 through 169 )A158 - 169 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 1 through 14 )B1 - 14 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 15 through 25 )B15 - 25 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 26 through 42 )B