Software Name Version Classification NB DENZOdata reductionShow SCALEPACKdata scalingShow REFMAC5.2.0019refinementShow PDB_EXTRACT3.006 data extractionShow SBC-Collectdata collection SHELXDphasing MLPHAREphasing DMphasing SOLVEphasing RESOLVEphasing HKL-3000phasing
Refinement Method to determine structure : SAD / Resolution : 2.1→50 Å / Cor.coef. Fo :Fc : 0.969 / Cor.coef. Fo :Fc free : 0.965 / Occupancy max : 1 / Occupancy min : 0.3 / SU B : 7.13 / SU ML : 0.095 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / σ(I) : 0 / ESU R : 0.134 / ESU R Free : 0.122 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.193 1225 5.1 % RANDOM Rwork 0.172 - - - all 0.173 23940 - - obs 0.173 23940 95.39 % -
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 : 69.42 Å2 / Biso mean : 49.399 Å2 / Biso min : 23.37 Å2 Baniso -1 Baniso -2 Baniso -3 1- -1.87 Å2 0 Å2 0 Å2 2- - -1.87 Å2 0 Å2 3- - - 3.75 Å2
Refinement step Cycle : LAST / Resolution : 2.1→50 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 1643 0 49 154 1846
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_d0.018 0.022 1826 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 1244 X-RAY DIFFRACTION r_angle_refined_deg1.705 1.997 2502 X-RAY DIFFRACTION r_angle_other_deg1.058 3 3063 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.278 5 242 X-RAY DIFFRACTION r_dihedral_angle_2_deg36.226 24.405 84 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.907 15 330 X-RAY DIFFRACTION r_dihedral_angle_4_deg17.189 15 15 X-RAY DIFFRACTION r_chiral_restr0.098 0.2 287 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.02 2036 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 349 X-RAY DIFFRACTION r_nbd_refined0.21 0.2 321 X-RAY DIFFRACTION r_nbd_other0.209 0.2 1301 X-RAY DIFFRACTION r_nbtor_refined0.17 0.2 831 X-RAY DIFFRACTION r_nbtor_other0.087 0.2 952 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.191 0.2 113 X-RAY DIFFRACTION r_symmetry_vdw_refined0.127 0.2 7 X-RAY DIFFRACTION r_symmetry_vdw_other0.272 0.2 24 X-RAY DIFFRACTION r_symmetry_hbond_refined0.217 0.2 6 X-RAY DIFFRACTION r_mcbond_it0.767 1.5 1382 X-RAY DIFFRACTION r_mcbond_other0.22 1.5 451 X-RAY DIFFRACTION r_mcangle_it0.995 2 1813 X-RAY DIFFRACTION r_scbond_it2.027 3 786 X-RAY DIFFRACTION r_scangle_it2.643 4.5 673
LS refinement shell Resolution : 2.095→2.149 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.339 67 - Rwork 0.268 1282 - all - 1349 - obs - 1349 73.92 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 19) 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 12.882 0.8622 6.3758 27.6135 10.0455 9.7356 0.2173 0.7586 -1.1854 -0.5668 -0.2329 0.6417 0.159 -0.2159 0.0157 -0.2014 0.056 0.0318 0.0115 -0.0034 -0.0449 38.2748 14.1714 12.422 2 19.0837 -10.4936 2.8085 8.8843 -7.8559 14.1683 -0.058 0.4534 0.4294 0.1698 -0.0367 -0.3453 -1.1662 0.877 0.0946 -0.0236 -0.0747 0.0208 -0.1178 0.0432 -0.0172 48.8794 22.801 18.8619 3 0.7953 -1.5282 -0.3277 4.6651 -3.6534 10.7469 -0.1245 0.2093 -0.0404 0.2736 0.1404 -0.3746 -0.3384 0.6265 -0.0158 -0.2014 -0.0025 0.0184 -0.1713 -0.0237 -0.053 49.006 14.0512 17.2449 4 6.928 -7.4182 1.2204 16.245 0.1243 2.3882 0.0472 0.5259 -0.4921 -0.2963 -0.15 -0.2715 0.41 -0.1382 0.1028 -0.1363 -0.0021 0.0416 -0.1366 -0.0456 -0.0184 44.9097 10.1712 11.9529 5 34.3578 -8.9044 -2.4918 8.0876 4.2425 17.8405 0.6881 0.839 2.68 -0.2258 0.2927 -0.3626 -1.2431 0.3729 -0.9809 -0.0201 0.0571 0.1218 -0.0496 0.0878 0.1717 42.7854 29.3596 11.207 6 13.9898 -6.5158 -5.6327 4.6489 1.2239 3.4815 0.3606 0.2023 0.6301 -0.3131 -0.0791 -0.3975 -0.4881 -0.1418 -0.2815 -0.12 0.0102 0.0077 -0.0854 0.0558 -0.1106 46.149 23.7353 9.4616 7 5.1207 -2.4704 1.3359 40.9289 19.8403 11.4424 0.0049 0.3787 0.1976 -0.7127 0.2509 1.3919 -0.5725 -0.3667 -0.2558 -0.0712 0.0747 0.0133 0.0653 0.1268 -0.003 31.9063 26.0961 11.403 8 6.8884 -3.0142 -1.3981 4.3831 3.0709 6.7239 0.0251 0.1114 0.1445 -0.017 0.1807 -0.0719 -0.3051 -0.022 -0.2058 -0.2403 0.0289 0.0133 -0.1524 0.0842 -0.0711 37.5174 19.8768 18.2802 9 52.5211 1.6429 1.5162 39.3915 9.0196 2.09 0.4541 1.7705 1.2766 -0.2089 1.5245 -4.0739 0.3298 1.7722 -1.9785 0.1249 0.006 0.0055 0.2782 -0.1852 0.5558 44.2673 35.6764 27.6672 10 4.0221 -2.2802 0.4564 8.5217 -0.3368 4.9746 -0.0763 -0.0667 0.421 0.0566 0.1685 -0.4894 -0.3276 0.2513 -0.0922 -0.1816 0.0741 0.0402 -0.1394 0.0435 0.0247 34.304 30.8774 25.4271 11 3.0458 0.1903 -0.6595 8.3259 -0.064 5.3184 0.115 0.5663 0.0515 -0.4386 -0.157 0.8235 -0.2621 -0.7749 0.042 -0.1852 0.0577 -0.0142 -0.0115 0.0234 0.0291 28.2017 18.23 17.7643 12 1.758 -0.612 -1.1622 3.3058 5.8129 10.226 -0.2488 0.0641 0.1578 -0.0802 0.1384 0.0991 -0.8053 -0.2964 0.1104 -0.1512 0.0299 0.0148 -0.188 -0.0016 0.0409 38.9396 18.6713 31.735 13 5.3832 0.9198 5.0245 17.7268 -6.9833 14.147 -0.2677 -0.6029 0.4211 0.5948 -0.0585 -1.2454 -0.115 1.1278 0.3262 -0.0943 0.1007 -0.0658 0.0004 -0.0825 0.1868 40.2123 28.8265 41.7571 14 13.0307 0.6579 6.6491 2.4541 1.9383 4.4537 -0.0225 -0.4633 -0.0612 0.175 0.0781 -0.0772 0.095 -0.0269 -0.0556 -0.1732 0.0622 -0.0023 -0.1783 0.0075 -0.0359 35.1045 24.441 33.7703 15 5.5133 -0.5634 0.5304 2.5566 0.3128 2.34 -0.1623 -0.1504 0.0413 0.117 0.1338 0.098 -0.1351 -0.1524 0.0284 -0.1892 0.0367 0.0145 -0.2266 0.036 -0.0983 35.8394 16.68 29.3595 16 8.8033 -1.7242 -5.3269 5.0064 0.2502 7.9334 -0.1345 -0.9216 -0.0505 0.5355 0.211 -0.2728 -0.055 0.7029 -0.0764 -0.1345 0.0608 -0.0991 -0.1105 0.0277 -0.0316 49.1479 11.4468 36.2938 17 9.0305 3.0373 3.49 4.1757 1.3987 4.2284 -0.0984 0.123 -0.1581 0.1927 0.0902 -0.2062 0.024 0.1497 0.0081 -0.206 0.03 -0.0032 -0.2235 0.0244 -0.0703 46.9871 11.0053 26.1073 18 2.3532 -1.5715 0.7321 2.5173 1.1084 1.9658 -0.06 -0.3439 -0.0403 0.3813 -0.0217 0.1439 0.1791 -0.1507 0.0818 -0.1587 0.0072 -0.0005 -0.1866 0.061 -0.0906 40.0574 8.8184 31.6632 19 17.8011 2.8185 4.001 9.4664 -4.0356 3.3161 0.0222 -0.8154 -0.2361 0.3034 0.0603 -0.2581 0.3073 0.0771 -0.0825 -0.1158 0.056 0.008 -0.1731 0.0092 -0.054 46.6296 1.4774 30.6689
Refinement TLS group Show large table (7 x 19) 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 AA0 - 6 21 - 27 2 X-RAY DIFFRACTION 2 AA7 - 14 28 - 35 3 X-RAY DIFFRACTION 3 AA15 - 20 36 - 41 4 X-RAY DIFFRACTION 4 AA21 - 29 42 - 50 5 X-RAY DIFFRACTION 5 AA30 - 34 51 - 55 6 X-RAY DIFFRACTION 6 AA35 - 54 56 - 75 7 X-RAY DIFFRACTION 7 AA55 - 62 76 - 83 8 X-RAY DIFFRACTION 8 AA63 - 74 84 - 95 9 X-RAY DIFFRACTION 9 AA75 - 80 96 - 101 10 X-RAY DIFFRACTION 10 AA81 - 91 102 - 112 11 X-RAY DIFFRACTION 11 AA92 - 105 113 - 126 12 X-RAY DIFFRACTION 12 AA106 - 114 127 - 135 13 X-RAY DIFFRACTION 13 AA115 - 125 136 - 146 14 X-RAY DIFFRACTION 14 AA126 - 135 147 - 156 15 X-RAY DIFFRACTION 15 AA136 - 154 157 - 175 16 X-RAY DIFFRACTION 16 AA155 - 171 176 - 192 17 X-RAY DIFFRACTION 17 AA172 - 190 193 - 211 18 X-RAY DIFFRACTION 18 AA191 - 202 212 - 223 19 X-RAY DIFFRACTION 19 AA203 - 213 224 - 234