Software Name Version Classification NB REFMAC5.2.0019refinementShow PDB_EXTRACT3.006 data extractionShow SBC-Collectdata collection HKL-3000data reduction HKL-3000data scaling SHELXDphasing MLPHAREphasing DMphasing SOLVEphasing RESOLVEphasing HKL-3000phasing
Refinement Method to determine structure : SAD / Resolution : 1.72→26.9 Å / Cor.coef. Fo :Fc : 0.966 / Cor.coef. Fo :Fc free : 0.946 / Occupancy max : 1 / Occupancy min : 0.4 / SU B : 4.348 / SU ML : 0.074 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / σ(I) : 0 / ESU R : 0.114 / ESU R Free : 0.113 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.212 1312 5.1 % RANDOM Rwork 0.169 - - - all 0.171 25732 - - obs 0.171 25732 99.34 % -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.2 Å / Solvent model : MASKDisplacement parameters Biso max : 52.15 Å2 / Biso mean : 24.153 Å2 / Biso min : 10.32 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.13 Å2 0 Å2 0.25 Å2 2- - -0.43 Å2 0 Å2 3- - - -0.63 Å2
Refinement step Cycle : LAST / Resolution : 1.72→26.9 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 1896 0 10 239 2145
Refine LS restraints Show large table (5 x 17) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.017 0.022 2082 X-RAY DIFFRACTION r_angle_refined_deg1.477 1.963 2832 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.592 5 276 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.24 25.051 99 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.305 15 375 X-RAY DIFFRACTION r_dihedral_angle_4_deg19.018 15 9 X-RAY DIFFRACTION r_chiral_restr0.106 0.2 306 X-RAY DIFFRACTION r_gen_planes_refined0.007 0.02 1596 X-RAY DIFFRACTION r_nbd_refined0.206 0.2 1021 X-RAY DIFFRACTION r_nbtor_refined0.302 0.2 1391 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.151 0.2 194 X-RAY DIFFRACTION r_symmetry_vdw_refined0.211 0.2 48 X-RAY DIFFRACTION r_symmetry_hbond_refined0.233 0.2 24 X-RAY DIFFRACTION r_mcbond_it0.808 1.5 1319 X-RAY DIFFRACTION r_mcangle_it1.284 2 2064 X-RAY DIFFRACTION r_scbond_it2.042 3 854 X-RAY DIFFRACTION r_scangle_it3.168 4.5 753
LS refinement shell Resolution : 1.72→1.765 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.291 93 - Rwork 0.239 1702 - all - 1795 - obs - 1795 94.23 %
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 5.6319 8.25 1.2267 13.7509 -1.5126 15.3778 -0.3464 -0.0452 -0.5632 0.1896 -0.0735 -1.4702 1.2324 1.197 0.4199 0.116 -0.0256 0.0409 -0.0076 0.0044 0.138 19.2718 68.502 10.9226 2 2.6909 -2.0391 1.4205 1.7943 -1.315 1.9938 0.079 -0.0283 -0.0275 0.1716 0.0028 0.1429 0.2929 -0.1245 -0.0818 -0.008 -0.0826 0.0211 -0.0779 0.0021 -0.0487 8.2408 70.6742 9.684 3 1.9129 1.3864 0.991 1.5158 1.1417 1.0682 0.0076 0.0535 0.1435 -0.017 -0.0417 0.1598 -0.0711 -0.1029 0.0341 -0.0692 -0.0063 -0.0052 -0.0218 0.0036 -0.0774 15.3768 84.4593 5.4676 4 1.5879 -1.2605 -0.9829 6.0887 0.8494 0.6094 0.0108 0.2645 -0.1072 0.1436 -0.1179 0.2065 -0.113 -0.1287 0.1071 0.0592 0.0422 -0.0256 -0.0565 -0.0037 -0.0448 17.26 104.949 25.0693 5 6.1012 0.869 -1.4019 3.1296 0.8795 0.7096 -0.1846 -0.1156 -0.112 0.2092 0.0877 0.4654 0.1873 0.1992 0.0969 -0.0147 0.023 -0.021 -0.0544 -0.0478 -0.0488 9.661 99.573 21.1627 6 1.2761 1.4576 -2.4834 3.5388 -2.1303 5.0992 -0.1998 -0.1823 -0.0561 0.197 0.0836 0.7648 0.3202 -0.4319 0.1161 0.2792 0.0323 0.0897 0.0552 -0.0373 0.335 1.8535 107.8914 26.2483 7 7.9824 -0.1962 -1.5352 6.4298 -0.1288 1.9953 -0.1396 0.3816 0.1485 -0.5151 -0.0745 0.5694 -0.3593 -0.1308 0.2141 0.1213 0.0531 -0.0681 -0.1592 -0.0055 -0.0548 7.6398 113.7795 18.6326 8 26.9345 -11.283 -10.4543 7.6835 5.989 7.5971 0.5293 0.9232 0.356 -0.663 -0.3852 -0.7286 -0.4397 -0.0362 -0.1441 0.1424 0.0308 0.0634 -0.1932 0.0176 -0.0621 21.6236 109.189 15.4887 9 4.3497 3.7161 3.6568 4.9595 3.6927 3.2555 0.0079 -0.1716 -0.0649 0.145 -0.0304 -0.0804 0.0534 -0.1473 0.0225 -0.0594 0.0183 -0.0048 -0.0477 0.0004 -0.0764 29.358 89.6761 7.093 10 2.3796 2.5374 2.0301 2.7056 2.1647 1.7319 -0.11 0.165 0.0351 0.0757 0.2093 -0.056 0.0527 -0.2058 -0.0993 -0.0668 0.009 -0.0002 -0.0329 0.0001 -0.0933 24.0415 82.1095 -3.1324 11 8.715 -2.0365 -3.5414 3.8631 7.3401 14.1301 0.0436 -0.258 1.0552 -0.5464 -0.0779 0.4052 -1.1308 0.0106 0.0343 0.0384 -0.004 -0.0151 -0.0002 0.0072 0.0624 16.4923 94.9007 4.1441 12 34.1692 14.7222 -30.7331 43.8772 7.8692 42.5849 1.4246 0.8459 2.6437 0.7384 -0.3997 2.7046 -3.1333 -0.3665 -1.0249 0.1415 0.0285 0.0578 0.0459 0.0829 0.1837 24.9645 100.5389 1.2253 13 6.4693 4.6508 -4.0604 11.2859 -0.1096 3.5423 -0.1423 0.4937 0.3205 -0.1849 0.1055 0.5904 -0.2863 -0.1935 0.0367 -0.0462 -0.0069 0.0054 -0.0162 0.0345 -0.073 25.0593 95.0514 -0.8235 14 23.4955 -5.6826 -18.4563 11.5061 23.3899 79.077 1.0183 1.4104 2.1127 -0.6315 0.0973 -1.3198 -2.0323 -0.0705 -1.1156 0.1686 0.0783 -0.0108 0.0886 0.1246 0.2493 13.1985 96.8151 0.3851 15 10.2659 1.7703 1.2157 8.0249 -8.3221 18.3698 0.0713 0.6349 0.9784 -0.9275 0.3533 0.1082 -1.9115 -0.8107 -0.4246 0.469 0.0858 -0.0202 0.1486 0.0213 0.2914 5.7299 99.2118 7.4099 16 1.5336 -1.0684 -0.8708 4.1326 3.4253 6.5409 0.0257 0.1908 0.3586 -0.1763 -0.0819 0.1967 -0.2181 -0.3397 0.0562 -0.1182 -0.0084 -0.0432 0.0071 0.0203 -0.034 6.4849 89.2841 2.7324 17 0.5637 0.1075 -0.1919 0.2023 -0.303 0.4556 -0.0073 -0.0146 -0.0096 0.0286 0.0085 0.0583 0.0213 -0.0355 -0.0012 -0.0655 -0.0078 -0.0048 -0.0461 -0.0095 -0.0595 13.4741 84.7579 13.2297 18 3.7923 -0.286 -0.4499 0.0219 0.0186 0.9046 -0.035 -0.0666 0.0367 0.0209 0.0474 -0.0301 0.0986 0.0064 -0.0125 -0.0447 -0.0125 -0.0051 -0.0478 0.0002 -0.0736 17.3173 81.0049 18.3338 19 0.1659 -0.6199 -0.8643 2.3165 3.23 4.5038 0.0121 -0.2541 -0.2869 0.0439 0.0287 -0.1325 0.1017 0.0733 -0.0408 -0.0435 0.01 -0.0091 -0.0658 0.0194 -0.0412 25.5967 77.2415 7.749 20 37.3544 -1.8348 2.5423 1.7653 -3.6219 7.6963 0.0383 1.7802 -1.3269 -1.2235 0.36 0.0357 0.5122 -0.0464 -0.3983 0.1686 -0.0318 0.0034 0.0896 -0.075 0.0876 17.9426 71.1633 0.6808
Refinement TLS group Show large table (7 x 20) 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 AA-2 - 3 1 - 6 2 X-RAY DIFFRACTION 2 AA4 - 12 7 - 15 3 X-RAY DIFFRACTION 3 AA13 - 34 16 - 37 4 X-RAY DIFFRACTION 4 AA35 - 57 38 - 60 5 X-RAY DIFFRACTION 5 AA58 - 73 61 - 76 6 X-RAY DIFFRACTION 6 AA74 - 84 77 - 87 7 X-RAY DIFFRACTION 7 AA85 - 90 88 - 93 8 X-RAY DIFFRACTION 8 AA91 - 103 94 - 106 9 X-RAY DIFFRACTION 9 AA104 - 115 107 - 118 10 X-RAY DIFFRACTION 10 AA116 - 122 119 - 125 11 X-RAY DIFFRACTION 11 AA123 - 135 126 - 138 12 X-RAY DIFFRACTION 12 AA136 - 140 139 - 143 13 X-RAY DIFFRACTION 13 AA141 - 149 144 - 152 14 X-RAY DIFFRACTION 14 AA150 - 155 153 - 158 15 X-RAY DIFFRACTION 15 AA156 - 162 159 - 165 16 X-RAY DIFFRACTION 16 AA163 - 179 166 - 182 17 X-RAY DIFFRACTION 17 AA180 - 211 183 - 214 18 X-RAY DIFFRACTION 18 AA212 - 228 215 - 231 19 X-RAY DIFFRACTION 19 AA229 - 237 232 - 240 20 X-RAY DIFFRACTION 20 AA238 - 243 241 - 246