Software Name Version Classification REFMAC5.3.0037refinement MAR345data collection DENZOdata reduction SCALEPACKdata scaling REFMACphasing
Refinement Method to determine structure : FOURIER SYNTHESISStarting model : PDB ENTRY 1R5DResolution : 1.69→27.77 Å / Cor.coef. Fo :Fc : 0.959 / Cor.coef. Fo :Fc free : 0.948 / SU B : 3.413 / SU ML : 0.061 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.108 / ESU R Free : 0.105 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.20428 1326 5 % RANDOM Rwork 0.16862 - - - obs 0.17036 25228 97.45 % -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.2 Å / Solvent model : MASKDisplacement parameters Biso mean : 14.364 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.07 Å2 0 Å2 0 Å2 2- - -0.1 Å2 0 Å2 3- - - 0.16 Å2
Refine analyze Luzzati coordinate error obs : 0.196 ÅRefinement step Cycle : LAST / Resolution : 1.69→27.77 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 1882 0 42 307 2231
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_d0.01 0.022 1972 X-RAY DIFFRACTION r_angle_refined_deg1.284 1.971 2661 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.844 5 246 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.825 24.865 74 X-RAY DIFFRACTION r_dihedral_angle_3_deg12.498 15 365 X-RAY DIFFRACTION r_dihedral_angle_4_deg11.941 15 8 X-RAY DIFFRACTION r_chiral_restr0.088 0.2 295 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 1420 X-RAY DIFFRACTION r_nbd_refined0.19 0.2 940 X-RAY DIFFRACTION r_nbtor_refined0.293 0.2 1347 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.133 0.2 232 X-RAY DIFFRACTION r_symmetry_vdw_refined0.157 0.2 56 X-RAY DIFFRACTION r_symmetry_hbond_refined0.137 0.2 34 X-RAY DIFFRACTION r_mcbond_it0.685 1.5 1274 X-RAY DIFFRACTION r_mcangle_it1.14 2 2013 X-RAY DIFFRACTION r_scbond_it1.862 3 777 X-RAY DIFFRACTION r_scangle_it2.907 4.5 648
LS refinement shell Resolution : 1.688→1.732 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.255 72 - Rwork 0.199 1706 - obs - - 89.21 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 24) 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 6.4828 -0.4176 -1.0676 1.8274 1.1575 9.1638 0.0796 -0.4102 0.0757 0.2785 -0.0813 -0.0981 0.078 0.4673 0.0018 0.0324 -0.0214 -0.011 0.053 0.0098 -0.0004 11.0869 19.5633 23.2512 2 6.1972 -2.9073 2.3211 6.9707 -5.0435 4.8553 0.1778 0.4762 0.2624 -0.4547 -0.1693 0.0383 0.2677 0.0696 -0.0084 0.0521 0.009 -0.0094 0.0481 0.0118 0.0134 6.9156 22.6248 9.5224 3 4.2087 1.3484 -0.0479 2.3685 -1.2108 3.6246 -0.0008 0.0879 0.0281 -0.2034 0.0584 0.2587 0.0907 -0.2203 -0.0576 0.0043 -0.0036 0.0018 0.0185 -0.0041 0.0407 18.6649 27.3673 5.5442 4 13.0913 -7.0931 -6.6838 14.0693 14.1338 14.2191 0.0627 -0.9927 0.0875 1.1964 -0.0782 0.0005 0.2167 -0.0585 0.0155 0.0693 -0.017 0.0203 0.1233 -0.0188 -0.0347 23.8402 32.1517 16.7676 5 3.1194 0.4774 -0.745 1.0691 0.003 1.1704 0.0336 0.0146 -0.0166 -0.0383 -0.0089 0.0142 -0.0322 -0.0311 -0.0247 0.0494 -0.0016 -0.0061 0.017 -0.0049 0.0458 34.0825 31.2999 1.6962 6 1.5409 -0.0243 -0.6415 5.4957 4.4445 6.3974 0.1397 -0.0063 0.0237 -0.1891 0.091 -0.1614 -0.3394 -0.0571 -0.2306 0.053 -0.0245 0.0083 -0.0114 0.0003 0.0146 42.9924 43.3913 3.1774 7 5.1531 2.3396 0.8043 3.0243 0.7488 2.2369 -0.0618 0.5198 -0.1585 -0.2375 0.1862 -0.1396 0.0255 0.1631 -0.1244 0.0771 0.0099 -0.0071 0.0446 0.0051 0.0235 36.4585 35.2873 -4.6086 8 3.5274 0.3059 -2.7376 3.9664 -1.7632 8.6895 0.5019 -0.0605 0.6684 0.2711 -0.0906 0.143 -0.6892 -0.6932 -0.4113 0.0133 0.0257 0.0281 0.0005 -0.0342 0.0905 18.1727 39.4369 6.4562 9 2.7156 -1.7351 -2.4921 2.2639 -2.825 19.1765 0.2919 -0.7885 -0.008 0.3345 0.393 0.6199 -0.1352 -0.5836 -0.6849 -0.0258 -0.0003 0.0762 0.0936 -0.0265 0.0503 15.3267 35.8232 14.5517 10 21.5334 5.1156 -19.4263 1.2188 -4.4461 25.7071 -0.1704 0.6104 -0.053 -0.1851 0.1398 0.2481 0.1969 -0.5929 0.0306 0.0618 0.0211 -0.0294 -0.0145 0.0344 0.057 22.0939 34.7179 -3.7659 11 5.042 -1.8934 4.7816 1.6843 -1.6916 5.8969 -0.1053 0.2611 0.0907 -0.0241 0.026 -0.0289 -0.198 0.1619 0.0793 0.0417 -0.0194 -0.0087 0.0233 0.0176 0.035 38.3472 37.1785 0.4721 12 5.2289 -4.1254 2.8667 4.6719 -1.6191 3.0472 -0.1375 -0.1416 0.2166 -0.012 0.1138 -0.1471 -0.0764 -0.0829 0.0238 0.0462 -0.0271 -0.0104 0.0256 0.0134 0.0594 39.9343 35.4128 5.0675 13 6.4253 0.5445 1.318 2.5131 -0.1408 3.2579 -0.0278 -0.4886 -0.1047 0.1884 -0.0784 -0.1099 -0.1123 -0.0107 0.1062 0.0256 -0.0116 -0.0021 0.0445 0.0174 0.0092 34.8746 28.5582 10.5551 14 2.9313 0.6319 -1.8076 0.8172 -0.5327 1.1447 -0.0968 0.3205 0.112 -0.1641 0.1165 -0.0078 -0.0019 -0.1276 -0.0197 0.034 -0.0186 0.0199 0.0343 -0.0093 0.0279 20.7197 20.698 0.6808 15 1.7061 1.7656 0.2725 3.9547 0.565 2.3952 0.1128 0.0777 -0.0253 -0.111 -0.0346 -0.0709 -0.0728 0.0973 -0.0782 0.0003 -0.0092 0.0122 0.0463 0.0085 0.0326 18.2891 20.9614 11.8511 16 20.5434 -17.45 1.7839 14.8991 -2.2824 7.8383 0.1082 -0.6337 -0.0959 0.8367 0.1442 -1.0039 -0.0407 0.9486 -0.2524 0.0076 -0.0322 -0.0856 0.1424 0.0224 0.0675 22.8318 15.8649 17.7353 17 2.0189 -0.191 -0.6396 1.2 -0.4131 1.6127 0.0375 -0.0276 -0.0508 0.0325 -0.0104 0.0136 0.0427 -0.0483 -0.0271 0.0533 0.0047 -0.012 0.0356 -0.0093 0.0396 3.6519 16.2411 14.5518 18 14.8873 -8.9893 8.0923 11.0608 -6.4416 4.8282 0.0453 0.0612 -0.4562 -0.0708 0.2005 0.3537 0.1129 0.0162 -0.2458 0.0591 -0.0307 -0.0118 0.0435 0.0312 -0.015 0.6474 2.9437 20.9532 19 2.1505 -0.6505 2.2531 6.4396 -6.9746 13.5071 0.0342 -0.0464 -0.1083 0.036 0.325 0.2979 0.0334 -0.4979 -0.3592 0.0033 -0.0067 0.0019 0.0459 0.0196 0.0173 -2.8123 8.9881 19.1714 20 7.7068 0.1993 -0.1154 1.8318 0.1732 1.5291 0.0125 0.0614 -0.197 -0.0667 0.0043 -0.1122 0.1627 0.0395 -0.0169 0.0927 0.0157 -0.0034 0.031 -0.0072 0.0139 8.5851 12.9531 7.1701 21 12.9803 3.9273 14.7368 16.5293 15.539 35.0339 0.0804 1.0311 -0.0486 -0.3018 -0.0371 -0.6878 0.3748 3.1176 -0.0432 -0.0681 0.1532 0.0629 0.2549 0.1087 0.0514 27.9989 10.0473 9.2945 22 11.1255 4.0877 -1.4602 3.2466 1.8673 4.3837 -0.091 0.6785 0.2306 -0.1921 0.0722 0.0113 0.2356 0.2154 0.0188 0.0597 0.0277 0.0121 0.0187 -0.0057 0.0289 15.59 12.7906 3.6568 23 2.1303 0.5352 0.4335 1.6484 -0.8183 8.56 0.0627 0.0992 -0.0433 -0.1644 0.0034 0.0243 0.3352 -0.139 -0.066 0.0621 0.0003 0.0046 0.0205 -0.0065 0.011 1.2652 11.0545 11.6749 24 1.0046 -0.7729 -1.2067 3.8356 3.7325 8.3925 0.0704 0.0078 -0.0582 0.0103 0.0331 0.0054 0.0557 -0.0271 -0.1035 0.0422 -0.0054 -0.0045 0.0314 0.0062 0.0184 2.5939 13.1464 21.198
Refinement TLS group Show large table (7 x 24) 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 AA1 - 11 1 - 11 2 X-RAY DIFFRACTION 2 AA12 - 18 12 - 18 3 X-RAY DIFFRACTION 3 AA19 - 33 19 - 33 4 X-RAY DIFFRACTION 4 AA34 - 39 34 - 39 5 X-RAY DIFFRACTION 5 AA40 - 59 40 - 59 6 X-RAY DIFFRACTION 6 AA60 - 71 60 - 71 7 X-RAY DIFFRACTION 7 AA72 - 82 72 - 82 8 X-RAY DIFFRACTION 8 AA83 - 90 83 - 90 9 X-RAY DIFFRACTION 9 AA91 - 97 91 - 97 10 X-RAY DIFFRACTION 10 AA98 - 103 98 - 103 11 X-RAY DIFFRACTION 11 AA104 - 112 104 - 112 12 X-RAY DIFFRACTION 12 AA113 - 124 113 - 124 13 X-RAY DIFFRACTION 13 BB1 - 14 1 - 14 14 X-RAY DIFFRACTION 14 BB15 - 27 15 - 27 15 X-RAY DIFFRACTION 15 BB28 - 33 28 - 33 16 X-RAY DIFFRACTION 16 BB34 - 39 34 - 39 17 X-RAY DIFFRACTION 17 BB40 - 61 40 - 61 18 X-RAY DIFFRACTION 18 BB62 - 68 62 - 68 19 X-RAY DIFFRACTION 19 BB69 - 77 69 - 77 20 X-RAY DIFFRACTION 20 BB78 - 86 78 - 86 21 X-RAY DIFFRACTION 21 BB87 - 95 87 - 95 22 X-RAY DIFFRACTION 22 BB96 - 101 96 - 101 23 X-RAY DIFFRACTION 23 BB102 - 110 102 - 110 24 X-RAY DIFFRACTION 24 BB111 - 124 111 - 124