Software Name Version Classification SBC-Collectdata collection HKL-3000data collection HKL-3000phasing SHELXDphasing MLPHAREphasing DMmodel building RESOLVEmodel building Cootmodel building PHENIX(phenix.refine: 1.9_1678)refinement HKL-3000data reduction HKL-3000data scaling DMphasing RESOLVEphasing
Refinement Method to determine structure : SAD / Resolution : 2.048→48.78 Å / Cross valid method : THROUGHOUT / σ(F) : 0 / Phase error : 18.61 / Stereochemistry target values : TWIN_LSQ_FRfactor Num. reflection % reflection Selection details Rfree 0.171 5145 5.04 % random Rwork 0.154 - - - obs 0.156 102060 96.96 % - all - 102060 - -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 28.3 Å2 Refinement step Cycle : LAST / Resolution : 2.048→48.78 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 10391 0 45 1068 11504
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.003 10712 X-RAY DIFFRACTION f_angle_d0.792 14645 X-RAY DIFFRACTION f_dihedral_angle_d12.679 3845 X-RAY DIFFRACTION f_chiral_restr0.051 1680 X-RAY DIFFRACTION f_plane_restr0.005 1931
LS refinement shell Refine-ID : X-RAY DIFFRACTION
Show large table (7 x 20) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection obs % reflection obs (%)2.0479-2.0832 0.2303 183 0.1981 3414 3597 65 2.0832-2.1211 0.2172 220 0.1954 4298 4518 82 2.1211-2.1619 0.2285 245 0.1952 4646 4891 89 2.1619-2.206 0.2134 258 0.1897 4799 5057 92 2.206-2.254 0.2168 253 0.1861 4924 5177 93 2.254-2.3064 0.211 244 0.181 4915 5159 94 2.3064-2.3641 0.2105 282 0.1772 4937 5219 94 2.3641-2.428 0.1936 264 0.1748 4965 5229 95 2.428-2.4995 0.1909 274 0.175 4953 5227 94 2.4995-2.5801 0.1955 258 0.1769 4981 5239 95 2.5801-2.6723 0.2092 270 0.1737 4985 5255 95 2.6723-2.7793 0.1977 263 0.1713 5010 5273 95 2.7793-2.9058 0.204 264 0.1695 4963 5227 95 2.9058-3.059 0.1803 256 0.1607 5002 5258 95 3.059-3.2506 0.1897 249 0.1539 5009 5258 95 3.2506-3.5015 0.1573 229 0.1463 5033 5262 96 3.5015-3.8537 0.146 265 0.1332 5034 5299 95 3.8537-4.4111 0.1214 269 0.1126 4976 5245 95 4.4111-5.5562 0.1266 273 0.1223 5012 5285 95 5.5562-48.7264 0.1745 286 0.1564 5082 5368 94
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 18) 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 0.8578 0.018 0.334 1.2055 -0.4981 1.5027 0.1019 -0.0616 0.0301 -0.0274 -0.0717 0.1348 -0.059 -0.2064 -0.0019 0.1334 -0.0197 0.0113 0.1223 0.001 0.1035 -28.1818 40.5508 26.4667 2 1.1059 0.407 -0.2465 1.2765 -0.2562 0.7908 0.1252 -0.2109 -0.1072 0.0693 -0.1201 0.0641 -0.0506 0.0786 -0.0208 0.1378 -0.0015 0.0097 0.1254 0.0004 0.1237 10.4017 50.2257 21.6686 3 1.0653 0.4765 -0.0838 0.3154 -0.1523 0.152 0.176 -0.1806 -0.0743 0.0547 -0.1005 -0.1104 0.0448 0.1209 -0.0375 0.192 -0.0671 0.0139 0.163 0.0088 0.1395 -14.9745 37.9044 33.3036 4 1.0163 0.0816 -0.5509 0.7623 -0.013 1.3721 -0.036 -0.008 0.1396 -0.064 0.0436 0.0745 -0.1804 -0.0819 0.0228 0.1216 -0.0167 -0.0059 0.1443 0.0065 0.1061 19.3024 87.9931 -41.2349 5 1.072 0.1935 -0.2151 1.1438 -0.1622 0.9774 -0.0529 0.106 -0.0125 -0.1253 0.0564 -0.078 -0.0489 0.0245 -0.0044 0.1451 -0.0039 -0.009 0.1533 0.0151 0.1367 9.5611 49.0494 -36.3827 6 0.385 0.5131 -0.3125 0.574 -0.3354 0.1284 -0.1585 0.0471 0.0298 -0.2847 0.173 0.0309 0.1756 -0.0825 -0.028 0.2214 -0.0835 0.0324 0.2126 0.0149 0.1794 17.6524 69.61 -49.6947 7 0.9328 -0.2889 -0.2408 1.0809 0.1391 1.2815 -0.1781 -0.0279 -0.0968 -0.1107 0.1353 -0.0485 -0.0215 0.0493 -0.0207 0.1408 -0.0732 0.013 0.1787 0.0165 0.0971 26.6205 80.8322 -45.8893 8 1.13 -0.0932 0.4981 0.9589 0.0348 1.1138 -0.0117 -0.1811 -0.1261 0.1763 0.0695 0.1497 0.033 -0.3955 -0.0064 0.1756 0.0091 0.013 0.228 0.0399 0.1599 -11.0519 25.0351 -2.3224 9 0.6671 -0.1694 -0.1043 0.6564 0.0499 1.1813 0.0744 0.0074 -0.1034 0.0824 -0.1099 -0.0514 0.1152 0.0993 -0.0061 0.1717 0.0357 -0.0107 0.1431 0.0382 0.1263 2.5947 26.1613 -4.2612 10 1.4397 -0.093 0.1137 2.8074 -0.0051 1.2312 -0.024 0.0883 0.2966 -0.1065 -0.0993 -0.0677 -0.2866 0.168 -0.0096 0.1773 0.0335 -0.0206 0.1802 0.0393 0.1573 17.8165 56.2608 -22.3031 11 0.4773 -0.33 0.1797 0.89 -0.4539 0.6162 -0.0699 -0.0236 0.0017 0.0226 0.0548 -0.0497 -0.0297 0.0627 0.0287 0.1043 0.0457 0.0041 0.1822 0.0075 0.1236 16.0579 40.0796 -19.9688 12 0.9079 0.3337 0.1296 0.5593 0.0267 0.4259 0.1743 0.0305 -0.2816 0.0114 -0.1183 -0.0325 0.3191 0.1238 -0.0373 0.2318 0.0812 -0.0081 0.1967 0.0473 0.2222 5.3555 16.6436 -9.2966 13 0.9363 -0.3286 0.333 0.7527 -0.3583 0.8115 0.1669 0.2614 -0.467 -0.0519 -0.0652 0.0076 0.3841 0.0684 -0.0091 0.2347 -0.002 -0.0439 0.0977 0.0008 0.2441 -5.7033 16.4799 -9.3027 14 0.8958 0.0263 -0.2726 1.2002 0.4881 1.3148 0.0172 0.1033 0.0389 -0.1486 -0.0034 -0.0811 -0.1729 0.027 0.0009 0.1754 0.0201 0.0304 0.1704 0.024 0.146 34.4015 66.8529 -11.881 15 2.2162 -0.6789 0.1273 0.7567 -0.0312 0.8941 -0.0472 0.0253 -0.1571 0.0201 -0.0105 0.0436 0.2715 -0.0888 0.0386 0.222 0.0163 0.0298 0.0791 -0.0054 0.0863 15.2443 42.3321 8.5006 16 0.7389 0.161 -0.5168 0.7551 0.0149 0.5382 0.1771 0.1057 0.0629 -0.1221 -0.1408 -0.0752 0.0927 0.0196 0.0118 0.1914 0.0499 0.0397 0.1391 0.0298 0.1308 19.8563 47.0154 3.1876 17 0.7199 0.3067 -0.1792 0.9155 0.0025 0.4638 -0.0023 0.0076 -0.0699 0.0342 0.0241 -0.2182 0.0869 0.2183 -0.0259 0.1628 0.073 0.0118 0.2292 0.0243 0.161 36.987 50.7988 -4.1482 18 0.889 -0.3007 -0.5352 0.9387 0.2989 1.0438 -0.0653 -0.0847 0.0843 0.0866 0.1055 -0.3657 0.0325 0.2573 0.0004 0.1874 -0.0042 0.0233 0.2232 -0.0165 0.2189 41.3081 66.5401 -2.6437
Refinement TLS group Show large table (4 x 18) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 163 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 164 through 257 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 258 through 361 )4 X-RAY DIFFRACTION 4 chain 'B' and (resid 1 through 163 )5 X-RAY DIFFRACTION 5 chain 'B' and (resid 164 through 257 )6 X-RAY DIFFRACTION 6 chain 'B' and (resid 258 through 313 )7 X-RAY DIFFRACTION 7 chain 'B' and (resid 314 through 361 )8 X-RAY DIFFRACTION 8 chain 'C' and (resid 10 through 123 )9 X-RAY DIFFRACTION 9 chain 'C' and (resid 124 through 165 )10 X-RAY DIFFRACTION 10 chain 'C' and (resid 166 through 185 )11 X-RAY DIFFRACTION 11 chain 'C' and (resid 186 through 265 )12 X-RAY DIFFRACTION 12 chain 'C' and (resid 266 through 313 )13 X-RAY DIFFRACTION 13 chain 'C' and (resid 314 through 361 )14 X-RAY DIFFRACTION 14 chain 'D' and (resid 9 through 165 )15 X-RAY DIFFRACTION 15 chain 'D' and (resid 166 through 209 )16 X-RAY DIFFRACTION 16 chain 'D'