Software Name Version Classification HKL-3000data collection MLPHAREphasing PHENIX(phenix.refine: 1.8.2_1309)refinement HKL-3000data reduction HKL-3000data scaling
Refinement Method to determine structure : SAD / Resolution : 1.797→28.141 Å / SU ML : 0.18 / σ(F) : 1.39 / Phase error : 20.35 / Stereochemistry target values : MLHLRfactor Num. reflection % reflection Rfree 0.2045 3787 4.98 % Rwork 0.1711 - - obs 0.1728 75979 87.26 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 1.797→28.141 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 4664 0 41 488 5193
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 4990 X-RAY DIFFRACTION f_angle_d0.982 6776 X-RAY DIFFRACTION f_dihedral_angle_d13.603 1877 X-RAY DIFFRACTION f_chiral_restr0.071 745 X-RAY DIFFRACTION f_plane_restr0.005 878
LS refinement shell Show large table (7 x 27) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.7965-1.8193 0.3017 60 0.2345 1072 X-RAY DIFFRACTION 36 1.8193-1.8432 0.2782 86 0.2232 1635 X-RAY DIFFRACTION 53 1.8432-1.8684 0.2529 96 0.2049 1718 X-RAY DIFFRACTION 57 1.8684-1.8951 0.266 101 0.2068 1861 X-RAY DIFFRACTION 62 1.8951-1.9234 0.2329 105 0.2035 2043 X-RAY DIFFRACTION 66 1.9234-1.9535 0.2533 92 0.1962 2122 X-RAY DIFFRACTION 70 1.9535-1.9855 0.2382 134 0.1941 2293 X-RAY DIFFRACTION 76 1.9855-2.0197 0.2634 121 0.1875 2472 X-RAY DIFFRACTION 81 2.0197-2.0564 0.2009 142 0.1911 2550 X-RAY DIFFRACTION 85 2.0564-2.096 0.2176 147 0.1936 2793 X-RAY DIFFRACTION 91 2.096-2.1387 0.2235 151 0.1895 2805 X-RAY DIFFRACTION 93 2.1387-2.1852 0.2157 137 0.1881 2979 X-RAY DIFFRACTION 96 2.1852-2.236 0.2213 165 0.1809 2968 X-RAY DIFFRACTION 98 2.236-2.2919 0.2419 142 0.1841 3009 X-RAY DIFFRACTION 99 2.2919-2.3539 0.2058 174 0.1784 3008 X-RAY DIFFRACTION 99 2.3539-2.4231 0.2358 164 0.1765 3090 X-RAY DIFFRACTION 100 2.4231-2.5013 0.2308 183 0.183 3001 X-RAY DIFFRACTION 100 2.5013-2.5906 0.2131 163 0.1736 3055 X-RAY DIFFRACTION 100 2.5906-2.6942 0.2094 176 0.1761 3034 X-RAY DIFFRACTION 100 2.6942-2.8168 0.2308 151 0.1745 3072 X-RAY DIFFRACTION 100 2.8168-2.9651 0.2196 147 0.1786 3076 X-RAY DIFFRACTION 100 2.9651-3.1506 0.1911 169 0.1759 3083 X-RAY DIFFRACTION 100 3.1506-3.3935 0.1836 146 0.17 3097 X-RAY DIFFRACTION 100 3.3935-3.7343 0.1929 171 0.1604 3048 X-RAY DIFFRACTION 100 3.7343-4.2731 0.1695 165 0.1445 3095 X-RAY DIFFRACTION 99 4.2731-5.3775 0.1537 150 0.1339 3122 X-RAY DIFFRACTION 99 5.3775-28.1447 0.1952 149 0.169 3091 X-RAY DIFFRACTION 95
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 20) 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 5.8257 0.4416 -4.325 6.3667 -1.0814 3.3643 0.064 0.2655 -0.3044 -0.4813 -0.011 -0.268 0.2449 0.069 -0.0298 0.2467 0.0175 -0.1466 0.1834 -0.0054 0.2259 27.3539 6.8819 30.7475 2 1.0257 -0.6072 0.1787 1.4486 -1.4761 1.7861 0.1403 -0.0649 0.0829 0.1059 -0.1004 -0.1522 -0.0863 0.1874 0.009 0.2326 -0.0196 -0.1344 0.1805 -0.0174 0.219 23.5481 24.6248 38.3254 3 1.3982 -0.4781 0.427 2.7477 0.0914 1.7574 0.0673 0.0616 0.0602 -0.1331 -0.1785 -0.649 -0.0343 0.4705 0.0311 0.172 -0.0301 -0.1307 0.2506 0.0498 0.2984 32.5869 22.5016 35.2662 4 1.9577 -0.3402 0.5422 1.4983 -0.6147 2.8819 0.0573 -0.0124 -0.0735 0.0773 -0.0719 -0.0792 0.1609 0.0612 -0.0359 0.1493 0.0019 -0.0694 0.1085 -0.0037 0.1573 17.9507 15.1227 31.3906 5 6.9466 -4.2513 5.4546 6.0345 -5.4109 6.8812 -0.0469 -0.0783 -0.1576 0.282 0.2152 0.3787 -0.1568 -0.1798 -0.1069 0.0949 -0.0334 0.0117 0.0864 -0.0098 0.1422 3.0589 22.2741 33.9552 6 0.6512 -0.5525 -0.7629 3.0461 -0.7097 3.8663 0.0397 0.0251 -0.0074 -0.1609 -0.1259 -0.1827 0.0452 0.2659 0.0727 0.1181 0.0027 -0.0544 0.1217 -0.0011 0.1167 13.4663 29.1746 11.1793 7 1.272 0.0145 -1.0089 1.959 -0.8374 1.8826 0.0718 0.0148 0.1803 0.2038 0.0076 -0.1081 -0.3499 0.1094 -0.0929 0.1459 -0.0277 -0.0402 0.1171 -0.0145 0.1644 14.5274 40.5224 16.7046 8 5.1448 -1.3901 4.8789 8.7083 -3.7245 8.3862 -0.1363 -0.4326 0.3985 0.4771 0.1187 0.4223 -0.606 -0.2982 0.058 0.1352 -0.0129 0.0102 0.1299 -0.0211 0.1925 2.8597 34.2973 24.9721 9 9.2795 0.5285 4.9794 5.0256 0.6736 9.451 0.0088 0.3487 0.4171 -0.3641 0.0673 0.0658 -0.3473 -0.1752 -0.0553 0.2329 0.053 0.1378 0.1422 0.0481 0.2083 -27.3224 28.9693 30.6613 10 0.8991 -0.4923 -0.692 0.4766 0.424 2.1547 0.1252 -0.0017 0.0161 0.1553 -0.0993 0.2129 0.0539 -0.2859 0.5153 0.2835 0.0008 0.2105 0.2007 -0.0074 0.2425 -26.3966 16.4725 39.0521 11 6.3789 1.059 0.5103 1.7551 0.108 2.6742 0.149 -0.0407 -0.1324 0.1181 -0.1392 0.0565 0.05 -0.0429 0.0017 0.2556 0.0114 0.1352 0.1356 0.0367 0.2033 -22.1984 8.9935 38.1066 12 5.1336 -2.2866 1.0798 2.4138 -1.0696 3.0312 -0.1196 -0.2152 -0.3901 0.1885 -0.0702 0.3867 0.1681 -0.2818 0.0553 0.2408 -0.0478 0.1541 0.1598 -0.0139 0.2348 -27.6999 5.2722 38.7494 13 4.4404 -0.7137 -1.3537 1.8668 0.4331 5.0334 -0.0968 0.2464 -0.135 0.0054 -0.2083 0.6289 0.1156 -0.574 0.2017 0.2489 -0.015 0.1483 0.2308 -0.0655 0.3153 -34.3883 16.3751 33.2607 14 6.5082 -2.9369 -2.6694 2.3361 2.2605 4.4174 0.0601 0.1013 0.1635 0.0912 -0.0762 0.3348 -0.1517 -0.4061 -0.0486 0.213 0.0236 0.0979 0.1486 0.007 0.2295 -26.6909 21.8132 29.1641 15 3.9775 -2.0595 -4.238 1.4608 2.4704 6.1974 -0.0279 -0.0635 -0.0112 0.1908 -0.0619 0.2324 0.1142 0.0003 0.1094 0.1787 -0.019 0.0613 0.1188 0.0124 0.186 -14.2765 20.5244 34.553 16 5.6971 -3.3869 -4.5895 5.7708 4.9921 6.7261 0.1295 -0.2323 0.1793 0.2173 0.2022 -0.2839 -0.0234 0.2395 -0.273 0.1139 -0.036 -0.0175 0.1173 0.0105 0.1793 -2.9949 13.4281 33.5059 17 1.2383 -0.6126 0.7904 3.3284 0.7286 3.9961 0.0301 0.009 0.0366 -0.1477 -0.0893 0.1681 -0.1113 -0.1838 0.0586 0.105 -0.0029 0.0408 0.1112 0.0059 0.0941 -13.1745 6.8828 11.3538 18 3.5545 0.356 -0.7094 2.9593 -0.4995 6.7938 0.0358 -0.2621 -0.2438 0.503 0.0454 0.3518 0.4412 -0.3536 -0.0408 0.1742 -0.0112 0.0601 0.128 0.0118 0.2085 -16.4558 -6.8207 18.6219 19 1.2913 0.9496 1.2101 3.1415 1.0021 1.1438 0.0617 0.0889 -0.0941 0.1074 0.0502 -0.0803 0.189 0.0425 -0.0676 0.0922 -0.0118 0.013 0.0994 0.0184 0.1006 -12.7321 -2.6494 15.0794 20 6.7064 -3.2202 -5.3309 3.9282 4.0835 8.6274 -0.1384 -0.2547 -0.4385 0.4306 0.0832 -0.3779 0.5276 0.3008 0.0612 0.1766 -0.0195 -0.0028 0.1405 0.0265 0.2373 -3.1621 1.7723 25.4139
Refinement TLS group Show large table (4 x 20) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 40 through 56 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 57 through 94 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 95 through 145 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 146 through 178 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 179 through 200 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 201 through 259 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 260 through 316 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 317 through 333 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 40 through 56 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 57 through 71 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 72 through 94 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 95 through 113 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 114 through 138 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 139 through 161 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 162 through 178 )16 X-RAY DIFFRACTION 16 chain 'B'