Software Name Version Classification REFMAC5.2 refinement SCALEPACKdata scaling CNSrefinement HKL-2000data collection HKL-2000data reduction CNSphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB Entry 1KQRResolution : 1.604→14.88 Å / Cor.coef. Fo :Fc : 0.972 / Cor.coef. Fo :Fc free : 0.96 / SU B : 3.263 / SU ML : 0.06 / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.093 / ESU R Free : 0.092 / Stereochemistry target values : MAXIMUM LIKELIHOODDetails : ATOM RECORDS CONTAIN THE SUM OF TLS AND RESIDUAL B FACTORSRfactor Num. reflection % reflection Selection details Rfree 0.19173 7761 5.1 % RANDOM Rwork 0.1579 - - - all 0.15961 145697 - - obs 0.15961 145697 100 % -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.4 Å / Solvent model : BABINET MODEL WITH MASKDisplacement parameters Biso mean : 24.907 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.35 Å2 -0.06 Å2 0.07 Å2 2- - -0.13 Å2 0 Å2 3- - - -0.2 Å2
Refine analyze Free Obs Luzzati coordinate error 0.21 Å 0.19 Å Luzzati d res low - 5 Å Luzzati sigma a 0.15 Å 0.14 Å
Refinement step Cycle : LAST / Resolution : 1.604→14.88 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 10616 0 48 1724 12388
Refine LS restraints Show large table (5 x 24) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.011 0.022 11089 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 9308 X-RAY DIFFRACTION r_angle_refined_deg1.31 1.919 15077 X-RAY DIFFRACTION r_angle_other_deg1.506 3 21835 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.684 5 1310 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.543 24.876 605 X-RAY DIFFRACTION r_dihedral_angle_3_deg11.706 15 1786 X-RAY DIFFRACTION r_dihedral_angle_4_deg7.243 15 56 X-RAY DIFFRACTION r_chiral_restr0.084 0.2 1596 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 12455 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 2313 X-RAY DIFFRACTION r_nbd_refined0.192 0.2 1715 X-RAY DIFFRACTION r_nbd_other0.185 0.2 9152 X-RAY DIFFRACTION r_nbtor_refined0.182 0.2 5270 X-RAY DIFFRACTION r_nbtor_other0.084 0.2 6441 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.139 0.2 1155 X-RAY DIFFRACTION r_symmetry_vdw_refined0.165 0.2 44 X-RAY DIFFRACTION r_symmetry_vdw_other0.205 0.2 285 X-RAY DIFFRACTION r_symmetry_hbond_refined0.151 0.2 112 X-RAY DIFFRACTION r_mcbond_it0.794 1.5 8490 X-RAY DIFFRACTION r_mcbond_other0.177 1.5 2668 X-RAY DIFFRACTION r_mcangle_it1.019 2 10781 X-RAY DIFFRACTION r_scbond_it1.789 3 5390 X-RAY DIFFRACTION r_scangle_it2.495 4.5 4295
LS refinement shell Resolution : 1.604→1.645 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.241 549 - Rwork 0.192 10013 - obs - - 100 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 32) 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 3.5595 0.3934 1.4293 6.538 0.3188 2.858 0.1524 -0.2695 -0.3406 0.1238 -0.0138 0.1807 0.3269 -0.1347 -0.1386 -0.1792 0.0033 -0.0387 -0.1632 0.0383 -0.1919 10.2862 12.2007 21.9078 2 1.2135 -0.3365 -0.2008 9.5038 3.2725 2.4836 0.0188 -0.0798 -0.1991 0.0041 -0.1925 0.555 0.1715 -0.3331 0.1737 -0.2059 -0.0055 -0.0247 -0.1464 0.0168 -0.1641 -0.0238 18.0227 16.9393 3 3.2243 -1.8943 1.0189 3.2085 -0.4034 2.0817 -0.0217 -0.2016 0.1808 -0.0345 0.0265 -0.1063 -0.219 -0.1912 -0.0048 -0.188 0.0051 -0.0091 -0.1756 0.0042 -0.1885 -3.9591 30.9555 13.0294 4 2.1667 -0.3809 0.1875 1.147 0.2403 1.1934 0.0055 -0.0124 0.1206 -0.0572 0.0058 -0.0902 -0.02 0.1609 -0.0113 -0.1895 -0.0078 -0.0032 -0.1686 0.0074 -0.1953 15.2325 24.432 16.0823 5 4.5189 1.5009 1.6945 8.2057 -0.2918 1.4814 0.1498 -0.2614 -0.3946 0.037 0.0106 0.3584 0.3505 -0.1064 -0.1604 -0.1281 -0.0186 -0.0457 -0.1518 0.0592 -0.1577 44.0787 -28.4391 21.1789 6 2.2207 -0.1064 -0.3052 8.2409 3.1215 2.5551 0.1002 -0.214 -0.3583 0.1001 -0.1661 0.4961 0.2267 -0.3638 0.0659 -0.1929 -0.0311 -0.0348 -0.1375 0.0508 -0.1156 33.6974 -22.7578 16.0972 7 2.1047 -1.0153 -0.0493 1.9074 -0.1865 1.4783 0.0412 -0.1034 -0.0213 -0.0603 0.0166 0.0755 -0.0101 -0.1888 -0.0578 -0.1931 -0.0045 -0.0176 -0.1561 0.0166 -0.1867 29.5991 -10.0201 12.3445 8 1.718 -0.7042 -0.0183 1.2446 0.3123 1.521 0.0508 -0.1364 0.0362 0.0795 0.0146 -0.1312 0.0302 0.1644 -0.0654 -0.1882 -0.0136 -0.0071 -0.1734 -0.0028 -0.1652 48.8955 -16.0254 15.5923 9 7.1344 -0.1192 -0.5274 3.7515 -1.5003 3.0937 -0.0559 0.2477 0.0302 -0.6271 0.2246 0.4236 0.287 -0.4687 -0.1687 0.0344 -0.0656 -0.0944 -0.0906 0.0473 -0.1518 25.1816 47.684 33.8919 10 8.7226 -2.1281 -2.4065 3.1338 1.7219 2.9665 -0.246 0.0763 -0.414 -0.3897 0.0714 0.3878 0.3428 -0.3576 0.1747 -0.0347 -0.0544 -0.0383 -0.1449 0.0061 -0.1554 28.9161 36.577 39.2087 11 0.3603 -1.2073 -0.1325 4.0459 0.388 3.2378 -0.0889 -0.0674 -0.1413 -0.3339 0.2143 -0.1149 0.1826 0.07 -0.1254 -0.1368 -0.0436 0.0089 -0.1456 -0.007 -0.1758 40.6595 30.32 43.3079 12 0.6005 0.7127 -0.1934 3.4831 -0.0151 0.6013 -0.1532 0.0933 0.0387 -0.5874 0.1994 -0.1805 -0.0625 -0.0415 -0.0462 -0.0568 -0.0429 0.0334 -0.1381 -0.0157 -0.1772 38.1536 50.2931 39.6032 13 7.3298 0.2541 0.3218 4.3267 -1.2311 2.654 -0.0571 -0.1477 -0.1338 -0.1184 0.0843 0.4218 0.0688 -0.3138 -0.0273 -0.1678 0.0152 -0.0546 -0.1768 0.0163 -0.1971 14.8663 8.5292 34.4816 14 7.2342 -1.7847 -1.964 2.9137 1.3228 2.2293 -0.1264 0.0323 -0.3903 -0.0847 -0.0313 0.4116 0.2739 -0.3153 0.1576 -0.1531 -0.0012 -0.0225 -0.1583 0.0173 -0.1676 17.4948 -3.2474 39.0574 15 0.535 -0.4654 0.6635 3.2334 -0.6013 0.823 -0.0533 -0.0034 -0.0877 -0.1037 0.049 -0.0842 0.1305 -0.0012 0.0043 -0.1872 0.0236 0.0139 -0.1698 0.0211 -0.1857 28.8183 -10.981 42.2707 16 0.4899 -0.5046 -0.182 2.7902 0.0381 1.5569 -0.0304 -0.0532 0.0722 -0.0981 0.0197 -0.2181 -0.1866 0.1058 0.0106 -0.1848 -0.0006 -0.0049 -0.1595 0.0006 -0.1842 28.341 9.4026 39.6929 17 6.8561 0.6974 -0.1495 4.094 1.1402 2.9116 -0.061 -0.1167 0.1444 -0.1356 0.0768 -0.4285 -0.0817 0.2813 -0.0158 -0.1581 0.019 0.0546 -0.1805 -0.0218 -0.195 -0.735 34.8592 79.8586 18 7.4248 -2.061 2.5878 3.0748 -1.3775 2.8645 -0.1041 0.0392 0.4123 -0.079 -0.0387 -0.4255 -0.2743 0.3514 0.1428 -0.1533 -0.0037 0.0226 -0.1571 -0.0222 -0.161 -3.3528 46.6384 84.4347 19 0.4482 -0.2462 -0.7184 3.653 0.9602 1.2424 -0.083 -0.0296 0.1266 -0.1041 0.068 0.0474 -0.1914 -0.0005 0.0151 -0.1887 0.0266 -0.0133 -0.1547 -0.0272 -0.1878 -14.5399 54.3211 87.7637 20 0.5471 -0.6148 0.1943 2.8172 0.0757 1.6566 -0.0288 -0.055 -0.0829 -0.0928 0.0246 0.2051 0.1768 -0.1069 0.0043 -0.185 -0.0006 0.0014 -0.1584 -0.0021 -0.1831 -14.1984 33.9798 85.0721 21 8.4347 0.0949 1.19 3.9336 1.4593 3.5634 -0.0538 0.3068 0.0966 -0.5509 0.1812 -0.3061 -0.2559 0.4834 -0.1274 0.0257 -0.0586 0.0731 -0.0749 -0.0519 -0.1662 9.959 77.1452 79.2892 22 9.4179 -1.9063 2.3415 2.5151 -1.7816 2.8742 -0.2602 0.0443 0.4219 -0.4238 0.0793 -0.3982 -0.3386 0.3488 0.1809 -0.0216 -0.051 0.0279 -0.1425 -0.0228 -0.1435 6.2329 88.2913 84.5901 23 0.8231 -1.3972 0.7061 4.227 -0.251 3.1481 0.0041 -0.0837 0.12 -0.3384 0.1992 0.1166 -0.1891 -0.0625 -0.2033 -0.1274 -0.0392 -0.0087 -0.1394 -0.0075 -0.1756 -5.5068 94.5193 88.7145 24 0.645 0.7614 0.1818 3.5857 -0.0016 0.6232 -0.1556 0.1081 -0.0312 -0.6091 0.1801 0.1797 0.0636 0.0301 -0.0245 -0.0497 -0.0454 -0.0419 -0.1358 0.0094 -0.1756 -3.0049 74.556 84.9829 25 4.607 1.3436 -1.2321 7.8034 0.1848 1.5989 0.1263 -0.2593 0.3945 0.0969 0.0083 -0.2991 -0.3379 0.1293 -0.1346 -0.1324 -0.0196 0.0405 -0.1471 -0.0654 -0.1637 33.895 -9.622 66.5455 26 2.0566 -0.1466 0.2423 8.4218 -3.0393 2.5696 0.1079 -0.1783 0.3172 0.0893 -0.1868 -0.4826 -0.223 0.3679 0.0789 -0.1931 -0.0316 0.0255 -0.1391 -0.0474 -0.1301 44.3012 -15.3021 61.4588 27 2.2006 -0.8438 -0.1628 1.4703 0.0399 1.5639 0.0047 -0.1331 0.0113 -0.0232 0.0011 -0.0739 -0.0019 0.1698 -0.0058 -0.1961 -0.0038 0.0139 -0.1698 -0.0163 -0.1809 48.4086 -28.0161 57.7247 28 1.5715 -0.6642 0.0003 1.2169 -0.2944 1.3964 0.0481 -0.1227 -0.033 0.0909 0.0068 0.1159 -0.0316 -0.1492 -0.0548 -0.1902 -0.016 -0.0004 -0.1728 0.0014 -0.1654 29.1072 -22.0458 60.984 29 3.399 0.7534 -1.6227 6.4592 -0.3907 3.0686 0.173 -0.2578 0.313 0.1192 -0.0613 -0.1569 -0.3286 0.1372 -0.1117 -0.1837 0.0015 0.0325 -0.1614 -0.0416 -0.1872 3.8593 31.2012 67.2803 30 1.3469 -0.5368 0.3561 9.1224 -3.1645 2.6019 0.0251 -0.0822 0.1881 -0.0107 -0.2126 -0.6149 -0.2056 0.3161 0.1875 -0.1998 -0.0083 0.0223 -0.1524 -0.0244 -0.1623 14.1794 25.4054 62.3621 31 3.1759 -2.3325 -0.648 2.5645 0.4747 2.2153 -0.0305 -0.1406 -0.1478 -0.0433 0.0231 0.0354 0.1882 0.2333 0.0074 -0.1925 0.0092 0.0031 -0.1809 -0.0021 -0.183 18.1825 12.6936 58.3055 32 2.2365 -0.406 -0.1735 1.0965 -0.361 1.2975 0.0037 -0.0202 -0.1325 -0.0583 0.0037 0.0955 0.0153 -0.1651 -0.0074 -0.1924 -0.0086 -0.0026 -0.1736 -0.0118 -0.1969 -1.0681 18.9779 61.4638
Refinement TLS group Show large table (7 x 88) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA167 - 176 108 - 117 2 X-RAY DIFFRACTION 1 AA185 - 194 126 - 135 3 X-RAY DIFFRACTION 2 AA139 - 157 80 - 98 4 X-RAY DIFFRACTION 2 AA96 - 105 37 - 46 5 X-RAY DIFFRACTION 3 AA111 - 135 52 - 76 6 X-RAY DIFFRACTION 4 AA60 - 95 1 - 36 7 X-RAY DIFFRACTION 4 AA106 - 110 47 - 51 8 X-RAY DIFFRACTION 4 AA136 - 138 77 - 79 9 X-RAY DIFFRACTION 4 AA158 - 166 99 - 107 10 X-RAY DIFFRACTION 4 AA177 - 184 118 - 125 11 X-RAY DIFFRACTION 4 AA195 - 223 136 - 164 12 X-RAY DIFFRACTION 5 BB167 - 176 108 - 117 13 X-RAY DIFFRACTION 5 BB185 - 194 126 - 135 14 X-RAY DIFFRACTION 6 BB139 - 157 80 - 98 15 X-RAY DIFFRACTION 6 BB96 - 105 37 - 46 16 X-RAY DIFFRACTION 7 BB111 - 135 52 - 76 17 X-RAY DIFFRACTION 8 BB60 - 95 1 - 36 18 X-RAY DIFFRACTION 8 BB106 - 110 47 - 51 19 X-RAY DIFFRACTION 8 BB136 - 138 77 - 79 20 X-RAY DIFFRACTION 8 BB158 - 166 99 - 107 21 X-RAY DIFFRACTION 8 BB177 - 184 118 - 125 22 X-RAY DIFFRACTION 8 BB195 - 223 136 - 164 23 X-RAY DIFFRACTION 9 CC167 - 176 108 - 117 24 X-RAY DIFFRACTION 9 CC185 - 194 126 - 135 25 X-RAY DIFFRACTION 10 CC139 - 157 80 - 98 26 X-RAY DIFFRACTION 10 CC96 - 105 37 - 46 27 X-RAY DIFFRACTION 11 CC111 - 135 52 - 76 28 X-RAY DIFFRACTION 12 CC60 - 95 1 - 36 29 X-RAY DIFFRACTION 12 CC106 - 110 47 - 51 30 X-RAY DIFFRACTION 12 CC136 - 138 77 - 79 31 X-RAY DIFFRACTION 12 CC158 - 166 99 - 107 32 X-RAY DIFFRACTION 12 CC177 - 184 118 - 125 33 X-RAY DIFFRACTION 12 CC195 - 223 136 - 164 34 X-RAY DIFFRACTION 13 DD167 - 176 108 - 117 35 X-RAY DIFFRACTION 13 DD185 - 194 126 - 135