Software Name Version Classification SERGUIdata collection PHASERphasing REFMAC5.2.0019refinement HKL-2000data reduction HKL-2000data scaling
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB ENTRY 3EJ3Resolution : 1.5→55.05 Å / Cor.coef. Fo :Fc : 0.947 / Cor.coef. Fo :Fc free : 0.927 / SU B : 2.815 / SU ML : 0.055 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.093 / ESU R Free : 0.094 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.24704 2850 5.1 % RANDOM Rwork 0.21119 - - - obs 0.21296 53285 97.41 % - all - 56135 - -
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 : 33.789 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.28 Å2 0 Å2 0 Å2 2- - -0.28 Å2 0 Å2 3- - - -1 Å2
Refinement step Cycle : LAST / Resolution : 1.5→55.05 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 2821 0 0 378 3199
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_d0.009 0.022 2956 X-RAY DIFFRACTION r_angle_refined_deg1.123 1.958 4012 X-RAY DIFFRACTION r_dihedral_angle_1_deg4.508 5 392 X-RAY DIFFRACTION r_dihedral_angle_2_deg38.948 23.407 135 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.437 15 531 X-RAY DIFFRACTION r_dihedral_angle_4_deg17.343 15 28 X-RAY DIFFRACTION r_chiral_restr0.081 0.2 466 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.02 2206 X-RAY DIFFRACTION r_nbd_refined0.19 0.2 1415 X-RAY DIFFRACTION r_nbtor_refined0.297 0.2 2028 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.138 0.2 297 X-RAY DIFFRACTION r_symmetry_vdw_refined0.129 0.2 35 X-RAY DIFFRACTION r_symmetry_hbond_refined0.125 0.2 27 X-RAY DIFFRACTION r_mcbond_it0.475 1.5 1919 X-RAY DIFFRACTION r_mcangle_it0.705 2 3015 X-RAY DIFFRACTION r_scbond_it1.264 3 1141 X-RAY DIFFRACTION r_scangle_it1.896 4.5 980
LS refinement shell Resolution : 1.5→1.535 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.241 191 - Rwork 0.209 3389 - obs - - 86.08 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 54) 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 36.4188 -2.6632 -1.5512 1.4994 -0.8246 0.8964 -0.0371 -0.2388 0.2061 0.0467 0.0951 0.333 -0.0544 -0.1201 -0.0581 -0.1549 -0.0082 0.0082 -0.1524 -0.0231 -0.0621 -13.5619 7.2138 -13.4527 2 9.9697 2.5155 -5.137 7.5828 -7.4285 8.0593 -0.2076 -0.2787 -0.2397 0.219 -0.2274 -0.4706 0.1735 0.1636 0.435 -0.1502 0.0089 -0.0027 -0.1259 0.0033 -0.1408 -0.7819 0.6225 -10.0933 3 11.6783 -3.4265 -5.5259 4.6925 0.5987 7.9081 -0.2888 -0.2756 -0.3857 0.3234 0.0768 0.1438 0.342 0.0887 0.212 -0.1348 0.0013 0.0242 -0.1229 0.0064 -0.1758 -9.659 -1.7429 -4.514 4 19.5866 -5.6924 -1.4008 10.8463 -3.7433 2.9405 -0.073 -0.1246 0.0735 -0.0139 -0.021 0.0823 -0.1039 -0.0315 0.094 -0.114 0.0338 0.0344 -0.1098 0.0011 -0.1626 -18.3021 7.2314 -3.243 5 19.5646 -2.7554 -7.7175 28.7432 5.4584 18.0121 -0.3248 -0.3469 -0.4605 0.2857 0.3895 0.8862 -0.0443 -0.7336 -0.0647 -0.1204 0.0701 0.0866 -0.0173 0.0421 -0.0075 -25.6307 10.4202 -4.0622 6 17.3399 -2.0478 -10.3992 20.6136 10.7175 22.496 -0.5226 -1.115 -0.5904 1.0162 -0.3346 0.6423 1.1169 -0.3933 0.8572 -0.0036 -0.0545 0.0826 0.0207 0.0347 0.0054 -25.9156 3.0243 -7.588 7 19.6001 -0.2808 -3.6673 2.5984 -0.8557 1.2175 -0.0442 0.2348 0.0199 -0.0582 0.0395 0.1018 0.0554 -0.0399 0.0047 -0.1743 -0.0181 -0.002 -0.147 -0.0267 -0.148 -10.0577 2.9089 -15.0469 8 6.1995 -2.7038 -4.7014 13.3482 3.2626 6.4502 0.1023 -0.2745 0.3218 0.133 0.0776 -0.6486 -0.1375 0.2018 -0.1799 -0.203 -0.0222 -0.0472 -0.1277 0.0254 -0.0756 2.78 12.486 -15.7719 9 3.1723 2.1287 -2.7154 19.2136 -9.6981 9.3857 0.002 -0.3397 0.0029 0.9305 -0.292 -0.7341 -0.2001 0.2554 0.29 -0.1473 -0.0029 -0.0733 -0.0505 0.0127 -0.0604 5.7089 7.5748 -11.3911 10 4.2029 -9.7469 -8.334 30.3539 20.6598 19.6653 0.1555 0.1169 0.0622 -0.2559 -0.1126 0.1317 0.1249 -0.0119 -0.0429 -0.1523 0.0376 -0.0335 -0.1304 -0.0001 -0.132 -8.5406 16.4969 -25.615 11 0.036 -0.6389 1.0771 11.3269 -19.0956 32.1925 0.3556 0.2931 0.455 0.6733 0.3342 0.7283 -0.3817 -0.5268 -0.6898 -0.0551 0.0393 0.0578 -0.0858 0.0679 0.0937 -13.0816 30.7336 -24.5291 12 7.7795 -3.8097 -3.0479 14.404 3.213 3.3649 0.0494 0.2406 0.0868 -0.4319 -0.0041 0.612 -0.105 -0.1779 -0.0452 -0.1219 0.0047 -0.0218 -0.1286 0.0383 -0.0415 -8.2371 28.3193 -31.2869 13 16.5155 -9.8056 -0.676 14.5508 3.7324 6.3054 0.2198 0.5492 0.449 -0.8048 -0.134 -0.505 -0.2986 0.3542 -0.0858 -0.0721 -0.0277 0.0358 -0.1189 0.0256 -0.0718 -0.6778 21.4497 -33.9527 14 15.0704 1.0546 5.7777 4.3634 3.3679 14.8265 0.0277 0.6615 0.0942 -0.53 -0.0226 -0.4584 0.3457 0.3937 -0.0051 -0.0437 0.0446 0.0908 0.0222 0.0306 -0.0168 2.973 14.9988 -36.1179 15 15.5721 0.2349 -4.2375 4.6466 1.1918 8.7733 -0.1008 0.9701 -0.4039 -0.5482 0.0997 -0.4689 0.3491 0.2473 0.0011 -0.0449 0.0381 0.0194 -0.0384 -0.0189 -0.1074 -5.917 13.7078 -36.5998 16 3.0871 -4.5998 -7.4302 6.9263 12.0211 30.3297 0.2374 0.1563 0.4044 0.0835 0.0668 0.0522 -0.546 -0.0686 -0.3042 -0.1454 0.0023 0.0287 -0.1306 -0.0015 -0.0591 -13.8074 22.9908 -21.085 17 25.2802 -6.894 12.176 5.7271 -3.8126 10.6513 -0.3071 -0.0327 0.0266 0.2953 0.1369 0.0012 -0.611 -0.0447 0.1702 -0.0334 -0.0193 0.0291 -0.1571 -0.0445 -0.0956 -9.8183 21.3662 -10.0975 18 25.8908 -23.6365 7.2681 35.3607 1.0183 6.2906 -0.473 -0.6461 0.7797 0.4409 0.1923 0.3228 -0.959 -0.3814 0.2807 0.1957 -0.0103 0.0101 -0.0438 -0.0794 0.0575 -9.181 26.1346 -4.9324 19 2.4135 -4.0015 5.1006 28.9646 -28.323 31.8167 0.0332 0.0239 0.0703 -0.0409 0.3229 0.2303 -0.2377 -0.5301 -0.3562 -0.1573 0.04 0.0371 -0.1157 -0.005 -0.1165 -15.7622 7.0399 -28.4946 20 0.3175 -1.2282 1.0518 9.7839 4.2041 17.0894 0.1237 0.1906 -0.1182 -0.3524 -0.0857 0.0268 0.3095 0.1338 -0.0381 -0.0666 -0.0149 -0.0278 -0.1299 -0.0112 -0.1098 -11.534 -7.4618 -25.3734 21 13.1384 0.4152 6.8884 10.0242 -4.2967 12.1491 0.1732 0.5219 -0.6172 -0.9745 -0.1854 0.1082 0.7234 0.4136 0.0122 0.0244 0.023 -0.0545 -0.1396 -0.0274 -0.1069 -13.8953 -7.079 -34.5537 22 9.3231 -9.0562 5.2968 12.2815 -1.7959 9.9742 0.2828 0.2364 0.1158 -0.5214 -0.0239 0.6245 0.2389 -0.3336 -0.2589 -0.0751 -0.0222 -0.0693 -0.0766 0.0003 -0.0515 -20.4619 0.6022 -35.7827 23 11.2923 -0.4792 -1.7747 26.0063 -2.5778 5.131 0.055 0.4251 -0.0532 -0.3909 -0.0706 0.2681 -0.3494 -0.3635 0.0156 -0.0303 0.073 -0.0773 -0.0034 -0.018 -0.0121 -24.9445 9.3094 -37.9655 24 25.875 -7.1673 9.4471 18.0987 5.645 30.1604 0.3769 1.5681 -0.3561 -1.0491 0.083 0.3785 0.0285 0.192 -0.4599 0.0268 0.0128 -0.0753 0.0015 -0.0228 -0.1039 -16.5098 9.4514 -41.7719 25 2.204 -3.3954 3.6519 8.6526 -10.1815 12.1875 0.0175 0.0398 0.0202 0.0289 -0.131 -0.1124 -0.1302 0.1174 0.1135 -0.1335 -0.0014 0.0034 -0.1344 -0.0088 -0.1474 -10.8755 2.0381 -26.906 26 14.0689 -4.8089 -0.076 4.7203 0.6772 7.9411 -0.1741 -0.4595 -0.4026 0.2017 0.1061 0.5995 0.2356 -0.5233 0.068 -0.1215 -0.0235 0.0408 -0.1431 0.0022 -0.0876 -17.1222 -3.485 -11.8859 27 1.4271 -2.7766 -1.1333 15.5915 12.8687 18.9536 0.0144 0.1356 -0.4117 -0.1237 -0.0555 0.4242 0.76 -0.2853 0.0411 -0.0252 -0.0575 0.0222 -0.1069 -0.0044 -0.036 -14.9045 -11.0773 -17.3479 28 51.0471 -4.7084 4.9583 3.1156 0.3355 2.5085 0.0697 0.16 -0.1154 0.1792 0.1164 -0.1765 -0.1894 -0.0619 -0.1862 -0.1464 -0.012 0.004 -0.1924 -0.0227 -0.051 -12.4375 12.0011 -13.5187 29 1.5728 0.5507 0.8912 7.7934 9.4643 11.5256 0.0241 -0.2787 0.225 -0.2849 -0.2503 0.4886 -0.8396 -0.4706 0.2263 0.0817 0.143 0.1467 0.0276 0.0323 0.0266 -24.997 19.7194 -8.7957 30 16.8166 -9.6044 5.4473 8.1664 -3.8562 10.82 -0.2149 -0.8646 0.4734 0.4689 0.2837 -0.0725 -0.821 -0.6619 -0.0689 0.0048 0.0375 0.0974 -0.0412 -0.0196 -0.052 -18.1218 19.3216 -3.3158 31 19.6817 -9.554 4.5756 21.8329 -2.5224 5.7484 0.0439 -0.9821 0.0355 0.5894 0.2497 -0.0089 -0.0628 -0.0871 -0.2936 -0.0953 -0.034 0.0119 -0.0581 -0.0097 -0.1364 -10.4593 11.7433 -1.4642 32 11.4238 6.9748 1.1728 11.142 -4.07 6.3259 0.2179 -0.4425 -0.5711 0.4986 -0.166 -0.2732 -0.2615 0.0824 -0.0519 0.0296 -0.0211 -0.0777 -0.0332 -0.0027 -0.056 -4.301 9.2151 -1.3504 33 21.1935 -2.4854 9.665 5.3457 -3.1356 10.5764 -0.0519 -0.2456 -0.0261 0.2362 -0.0247 -0.3286 -0.1712 0.4662 0.0766 -0.1204 -0.0119 -0.0051 -0.1406 -0.0234 -0.1003 -5.6821 15.3583 -8.943 34 32.4161 8.5505 20.5096 3.0036 6.5506 14.7154 -0.0615 -0.447 0.4051 0.1983 -0.1911 0.3949 -0.2124 -0.7156 0.2526 -0.1446 0.0402 0.0277 -0.0651 0.0016 -0.0346 -23.7256 16.0249 -15.8626 35 7.9258 -7.1402 2.0154 26.1006 -5.2107 5.5058 0.1048 0.1016 -0.1198 0.4147 -0.2404 0.7264 -0.1103 -0.1775 0.1356 -0.1695 -0.0234 0.0585 0.0082 -0.0042 0.0118 -27.6021 7.0477 -19.1284 36 9.3319 -11.9525 -4.9534 24.1625 6.4427 11.2832 0.5447 -0.0027 -0.0384 -0.54 -0.3185 1.3229 -0.6491 -0.3809 -0.2262 -0.0553 -0.0881 0.0509 0.1586 0.0297 0.2719 -33.2252 4.7591 -18.85 37 2.0787 -4.7799 -2.6257 18.9155 11.0031 7.7599 -0.0209 -0.0593 0.0957 -0.1188 0.0532 -0.2351 -0.2013 0.1502 -0.0322 -0.1486 0.0113 -0.0033 -0.1241 0.004 -0.1186 -3.3399 10.4214 -24.987 38 7.8392 9.3997 3.5242 17.864 8.8483 7.6109 0.0187 0.2592 -0.7216 -0.1437 0.1799 -1.2008 -0.0458 0.6249 -0.1986 -0.1188 0.0165 0.0808 -0.0784 0.0346 0.0467 8.7109 8.247 -27.7079 39 1.9251 -3.4297 -0.6637 16.4997 -2.8605 3.1235 0.1053 0.034 0.0474 0.2316 -0.1688 -0.0935 -0.0763 0.0607 0.0635 -0.191 -0.0273 0.0136 -0.1208 0.042 -0.0523 5.4333 15.894 -24.4729 40 30.5223 -9.6507 3.1823 23.957 3.5329 5.289 -0.0742 0.0531 0.4778 -0.1578 0.1041 -0.252 -0.023 0.2024 -0.0298 -0.1315 -0.0208 0.0388 -0.1254 0.0497 -0.0856 1.0457 25.0748 -23.9088 41 8.9167 -7.4164 7.4361 15.3808 -6.1668 11.8047 -0.0211 0.0061 0.1156 0.3628 -0.258 -0.2825 -0.4528 0.2637 0.2791 -0.0941 -0.058 0.0046 -0.1093 0.0238 0.054 -0.6985 28.1452 -19.2406 42 2.9451 -0.4301 -0.4853 24.573 7.9332 6.9677 -0.0522 -0.2051 0.2691 0.4904 0.2106 -0.4026 -0.304 0.2728 -0.1584 -0.1453 -0.0033 -0.0248 -0.1363 0.0071 -0.1136 -1.3626 17.5499 -17.0223 43 2.8505 2.2203 3.4335 3.5646 3.1553 6.8308 0.3216 0.0598 -0.12 0.0079 -0.1043 -0.2744 0.3037 -0.1051 -0.2173 -0.1075 0.0241 0.0059 -0.146 -0.0097 -0.1382 -4.7996 1.5932 -27.9565 44 11.9911 0.8699 7.568 13.914 1.6193 13.199 0.0403 0.5549 0.2028 -1.254 -0.0789 0.282 -0.117 0.0397 0.0385 -0.0514 0.0479 0.0067 -0.1067 -0.0225 -0.1368 -9.6093 4.5813 -38.4253 45 24.7122 6.393 4.1554 8.6531 0.9523 5.2165 0.4364 -0.2137 -0.5217 -0.1169 -0.1795 -1.2725 0.1016 0.9063 -0.2569 -0.0007 0.0457 0.0439 0.0789 -0.0349 0.0267 1.7538 1.0451 -34.7485 46 7.4654 -8.7572 1.1422 39.5536 -22.0565 22.9118 -0.1585 -0.3202 -0.2498 -0.0805 0.1525 0.1632 0.1469 -0.3731 0.0059 -0.1979 0.0229 0.0485 -0.1044 0.0041 -0.0829 -19.1563 4.9087 -23.586 47 1.3737 2.8452 1.7604 10.96 -4.6456 15.8241 -0.2826 0.1846 0.4775 -0.0873 -0.043 0.9007 -0.5602 -0.6753 0.3256 -0.0915 0.0754 -0.0312 -0.061 -0.0319 0.0222 -23.881 16.3339 -30.9234 48 25.2348 12.0485 -12.5532 74.6608 -2.8356 6.3894 0.1943 0.3117 1.0696 0.0984 0.6474 2.9553 0.1061 -2.0392 -0.8417 -0.2172 0.1422 -0.0934 0.2532 0.1025 0.2816 -33.2641 12.1446 -30.0799 49 7.959 -4.3784 -1.3783 14.3942 1.3105 6.3332 -0.0896 0.3041 -0.1366 -0.8931 0.2779 1.2492 0.3166 -0.8777 -0.1884 -0.0357 -0.0994 -0.0949 0.1148 0.0345 0.0921 -29.1318 2.3664 -29.3814 50 2.7709 1.0918 -5.8219 6.3646 1.0779 14.1485 -0.5434 0.1145 -0.7893 -0.4718 -0.1856 -0.0224 1.4393 -0.682 0.729 0.1464 -0.107 0.0438 0.0111 -0.0243 0.1831 -24.1487 -6.958 -26.7392 51 5.9046 0.6457 1.1122 15.4444 7.4892 6.8276 0.2493 -0.1698 -0.6058 0.223 -0.2448 0.392 1.0968 -0.3938 -0.0045 -0.084 -0.0652 0.0217 -0.0448 0.0275 0.0129 -24.4551 -1.3927 -19.7984 52 5.272 7.7715 -5.5782 23.7511 -14.6741 9.2872 0.0287 0.2887 0.3494 -0.1385 0.137 0.7904 -0.0956 -0.3977 -0.1657 -0.0961 0.048 -0.0099 -0.0923 -0.0211 -0.043 -21.6167 16.5156 -27.7304 53 10.6508 -4.731 -5.2037 12.3781 6.0243 9.9317 0.2158 0.431 0.2343 -0.1758 -0.1105 -0.0123 -0.1251 -0.324 -0.1053 -0.0737 0.0268 -0.0576 -0.0589 0.0248 -0.1246 -12.5379 18.6995 -34.9802 54 9.3926 -2.6415 6.8196 28.5611 -12.6741 10.6506 -0.4466 0.0562 0.5987 -0.8753 0.782 0.5643 -0.961 -1.0945 -0.3353 0.1136 0.0663 -0.0004 0.0942 0.0706 0.019 -12.957 21.9984 -40.0575
Refinement TLS group Show large table (5 x 54) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A2 - 8 2 X-RAY DIFFRACTION 2 A9 - 13 3 X-RAY DIFFRACTION 3 A14 - 22 4 X-RAY DIFFRACTION 4 A23 - 28 5 X-RAY DIFFRACTION 5 A29 - 34 6 X-RAY DIFFRACTION 6 A35 - 39 7 X-RAY DIFFRACTION 7 A40 - 47 8 X-RAY DIFFRACTION 8 A48 - 54 9 X-RAY DIFFRACTION 9 A55 - 62 10 X-RAY DIFFRACTION 10 B2 - 8 11 X-RAY DIFFRACTION 11 B9 - 14 12 X-RAY DIFFRACTION 12 B15 - 21 13 X-RAY DIFFRACTION 13 B22 - 29 14 X-RAY DIFFRACTION 14 B30 - 36 15 X-RAY DIFFRACTION 15 B37 - 41 16 X-RAY DIFFRACTION 16 B42 - 48 17 X-RAY DIFFRACTION 17 B49 - 55 18 X-RAY DIFFRACTION 18 B56 - 59 19 X-RAY DIFFRACTION 19 C2 - 7 20 X-RAY DIFFRACTION 20 C8 - 14 21 X-RAY DIFFRACTION 21 C15 - 19 22 X-RAY DIFFRACTION 22 C20 - 26 23 X-RAY DIFFRACTION 23 C27 - 34 24 X-RAY DIFFRACTION 24 C35 - 39 25 X-RAY DIFFRACTION 25 C40 - 47 26 X-RAY DIFFRACTION 26 C48 - 56 27 X-RAY DIFFRACTION 27 C57 - 63 28 X-RAY DIFFRACTION 28 D2 - 7 29 X-RAY DIFFRACTION 29 D8 - 15 30 X-RAY DIFFRACTION 30 D16 - 22 31 X-RAY DIFFRACTION 31 D23 - 29 32 X-RAY DIFFRACTION 32 D30 - 36 33 X-RAY DIFFRACTION 33 D37 - 42 34 X-RAY DIFFRACTION 34 D43 - 48 35 X-RAY DIFFRACTION 35 D49 - 54 36 X-RAY DIFFRACTION 36 D55 - 58 37 X-RAY DIFFRACTION 37 E2 - 10 38 X-RAY DIFFRACTION 38 E11 - 16 39 X-RAY DIFFRACTION 39 E17 - 24 40 X-RAY DIFFRACTION 40 E25 - 29 41 X-RAY DIFFRACTION 41 E30 - 36 42 X-RAY DIFFRACTION 42 E37 - 43 43 X-RAY DIFFRACTION 43 E44 - 50 44 X-RAY DIFFRACTION 44 E51 - 56 45 X-RAY DIFFRACTION 45 E57 - 64 46 X-RAY DIFFRACTION 46 F2 - 6 47 X-RAY DIFFRACTION 47 F7 - 12 48 X-RAY DIFFRACTION 48 F13 - 18 49 X-RAY DIFFRACTION 49 F19 - 27 50 X-RAY DIFFRACTION 50 F28 - 36 51 X-RAY DIFFRACTION 51 F37 - 41 52 X-RAY DIFFRACTION 52 F42 - 48 53 X-RAY DIFFRACTION 53 F49 - 55 54 X-RAY DIFFRACTION 54 F56 - 58