Software Name Version Classification REFMAC5.8.0267refinement XDSdata reduction XSCALEdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2→60.05 Å / Cor.coef. Fo :Fc : 0.9 / Cor.coef. Fo :Fc free : 0.873 / SU B : 6.504 / SU ML : 0.109 / Cross valid method : FREE R-VALUE / ESU R : 0.048 / ESU R Free : 0.041 Details : Hydrogens have been added in their riding positionsRfactor Num. reflection % reflection Rfree 0.2687 2154 4.984 % Rwork 0.2274 41062 - all 0.229 - - obs - 43216 98.868 %
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.2 Å / Solvent model : BABINET MODEL PLUS MASKDisplacement parameters Biso mean : 28.482 Å2 Baniso -1 Baniso -2 Baniso -3 1- 3.426 Å2 0 Å2 0 Å2 2- - 3.426 Å2 0 Å2 3- - - -6.852 Å2
Refinement step Cycle : LAST / Resolution : 2→60.05 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 4452 0 75 410 4937
Refine LS restraints Show large table (5 x 31) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.005 0.013 4754 X-RAY DIFFRACTION r_bond_other_d0.001 0.015 4275 X-RAY DIFFRACTION r_angle_refined_deg1.281 1.641 6478 X-RAY DIFFRACTION r_angle_other_deg1.168 1.587 9868 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.543 5 565 X-RAY DIFFRACTION r_dihedral_angle_2_deg33.618 21.557 289 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.281 15 751 X-RAY DIFFRACTION r_dihedral_angle_4_deg20.256 15 39 X-RAY DIFFRACTION r_chiral_restr0.06 0.2 574 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 5555 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 1147 X-RAY DIFFRACTION r_nbd_refined0.184 0.2 1069 X-RAY DIFFRACTION r_symmetry_nbd_other0.177 0.2 4207 X-RAY DIFFRACTION r_nbtor_refined0.161 0.2 2205 X-RAY DIFFRACTION r_symmetry_nbtor_other0.074 0.2 2202 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.206 0.2 377 X-RAY DIFFRACTION r_symmetry_xyhbond_nbd_other0.167 0.2 2 X-RAY DIFFRACTION r_symmetry_nbd_refined0.29 0.2 25 X-RAY DIFFRACTION r_nbd_other0.303 0.2 79 X-RAY DIFFRACTION r_symmetry_xyhbond_nbd_refined0.252 0.2 9 X-RAY DIFFRACTION r_mcbond_it0.391 1.588 2215 X-RAY DIFFRACTION r_mcbond_other0.391 1.588 2216 X-RAY DIFFRACTION r_mcangle_it0.611 2.379 2776 X-RAY DIFFRACTION r_mcangle_other0.611 2.379 2775 X-RAY DIFFRACTION r_scbond_it0.401 1.638 2539 X-RAY DIFFRACTION r_scbond_other0.401 1.639 2540 X-RAY DIFFRACTION r_scangle_it0.595 2.441 3695 X-RAY DIFFRACTION r_scangle_other0.595 2.442 3696 X-RAY DIFFRACTION r_lrange_it3.072 30.679 20842 X-RAY DIFFRACTION r_lrange_other2.806 30.278 20550 X-RAY DIFFRACTION r_ncsr_local_group_10.058 0.05 9738
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Refine-ID Type Rms dev position (Å)Weight position 1 1 AAAX-RAY DIFFRACTION Local ncs0.05783 0.0501 1 2 BBBX-RAY DIFFRACTION Local ncs0.05783 0.0501
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 20
Show large table (11 x 20) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Rfactor all Num. reflection all Fsc free Fsc work % reflection obs (%)WRfactor Rwork 2-2.052 0.318 152 0.24 2971 0.244 3183 0.969 0.983 98.115 0.233 2.052-2.108 0.296 155 0.229 2952 0.233 3117 0.976 0.985 99.6792 0.222 2.108-2.169 0.273 147 0.23 2838 0.232 3019 0.974 0.983 98.8738 0.22 2.169-2.235 0.327 139 0.226 2739 0.231 2960 0.962 0.981 97.2297 0.217 2.235-2.308 0.261 145 0.215 2691 0.217 2848 0.973 0.983 99.5787 0.204 2.308-2.389 0.263 132 0.217 2599 0.219 2752 0.968 0.98 99.2369 0.206 2.389-2.479 0.271 134 0.235 2541 0.237 2678 0.956 0.969 99.888 0.224 2.479-2.579 0.273 124 0.222 2436 0.224 2571 0.959 0.972 99.5721 0.212 2.579-2.693 0.27 120 0.225 2304 0.227 2474 0.957 0.97 97.979 0.212 2.693-2.824 0.244 119 0.224 2244 0.225 2373 0.959 0.966 99.5786 0.212 2.824-2.976 0.263 115 0.242 2139 0.243 2266 0.945 0.95 99.4704 0.233 2.976-3.155 0.262 104 0.232 2004 0.234 2117 0.936 0.953 99.5749 0.224 3.155-3.37 0.269 100 0.232 1895 0.233 2010 0.937 0.951 99.2537 0.225 3.37-3.638 0.296 95 0.224 1749 0.228 1883 0.912 0.955 97.9288 0.22 3.638-3.981 0.266 85 0.218 1633 0.221 1737 0.936 0.953 98.9062 0.217 3.981-4.443 0.238 80 0.215 1485 0.217 1587 0.943 0.956 98.6137 0.215 4.443-5.117 0.244 68 0.221 1298 0.222 1396 0.949 0.954 97.851 0.222 5.117-6.234 0.262 61 0.239 1118 0.24 1210 0.958 0.951 97.438 0.244 6.234-8.679 0.29 50 0.25 889 0.252 953 0.93 0.943 98.5309 0.253 8.679-35.005 0.268 29 0.24 537 0.241 577 0.962 0.948 98.0936 0.257
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 40) 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 12.0017 -7.5257 -4.3218 10.0029 4.3268 5.7267 -0.3166 -0.4287 0.1514 0.4128 0.3742 -0.242 0.1566 0.2146 -0.0576 0.1844 -0.0015 -0.0223 0.1544 0.0489 0.1547 -54.3313 25.9883 13.0757 2 2.1047 1.0042 2.5147 11.5344 1.6986 3.9632 -0.0032 0.1163 -0.3296 -0.0333 0.2202 -0.0358 0.2356 0.524 -0.217 0.2401 0.0046 -0.0116 0.2086 0.0712 0.2591 -47.258 15.82 3.7763 3 3.4492 -3.2724 1.4329 3.1698 -1.5496 1.1564 0.0208 -0.3734 -0.0605 -0.0245 0.3183 0.1529 0.0014 -0.1067 -0.3391 0.2611 -0.0032 -0.0174 0.1289 0.0392 0.2344 -56.2681 25.0348 8.394 4 12.2288 -11.3824 3.5439 12.151 -6.8781 11.8919 -0.2052 -0.5837 0.6743 0.1763 0.1878 -0.4501 0.4642 -0.5035 0.0174 0.2566 -0.1764 0.0908 0.6043 -0.0811 0.3695 -68.5273 24.4643 9.3454 5 1.8467 -0.0896 -0.8515 2.6167 -0.427 1.3439 -0.0869 -0.3702 -0.111 0.0223 0.1065 0.234 0.1914 -0.1244 -0.0196 0.1159 -0.0173 -0.047 0.1726 0.0414 0.0857 -54.7476 32.2817 2.2397 6 5.9872 4.1721 -1.5131 2.9464 -0.9822 0.5227 0.1483 -0.094 -0.0214 0.2093 -0.1586 0.0075 0.1271 -0.1508 0.0103 0.2791 -0.1467 0.046 0.2855 0.028 0.1156 -61.964 30.424 6.022 7 4.9966 -2.5385 -2.0121 5.9981 2.803 1.494 -0.3335 -0.5425 -0.1282 0.1715 0.4747 -0.4277 0.1772 0.3197 -0.1413 0.2048 0.119 -0.0573 0.1906 0.0473 0.1603 -41.7925 24.6537 2.0449 8 8.0429 -0.3771 -0.1251 1.3664 -0.4109 0.3308 -0.0153 0.157 -0.6696 -0.4182 0.0197 0.0359 0.3565 0.0355 -0.0045 0.3893 0.0344 -0.026 0.0758 -0.0103 0.1649 -48.4476 21.2743 -7.5762 9 10.8869 3.5482 -0.4256 3.175 0.39 0.1636 0.1002 0.1341 0.221 0.2244 -0.0604 0.1192 0.0808 -0.0405 -0.0398 0.2601 -0.02 -0.0311 0.1374 0.0764 0.2671 -58.988 17.2266 0.7412 10 2.6945 1.3633 0.1455 3.5781 -0.0836 1.5688 -0.034 0.2114 -0.1581 -0.0821 0.1141 -0.0249 0.2684 -0.0818 -0.0801 0.1212 0.0154 -0.0351 0.0461 0.0022 0.0794 -56.6691 30.8643 -10.6008 11 5.1055 -4.2626 6.2827 4.7091 -4.2114 8.6899 0.0126 0.2389 -0.0206 -0.1731 0.1128 -0.1646 -0.1375 0.5208 -0.1254 0.0503 -0.0155 0.0336 0.2544 -0.0923 0.2308 -34.7694 37.9805 -11.0653 12 8.0745 -4.4451 0.0463 3.071 1.745 5.2106 0.1883 0.01 0.1641 -0.0807 0.1134 -0.2688 -0.0039 0.3353 -0.3017 0.1081 0.0273 -0.0356 0.1358 -0.0388 0.2929 -34.034 40.9506 -4.0148 13 1.1846 0.0526 0.4307 6.2057 -0.7067 1.7639 0.095 -0.2506 0.0924 0.1267 0.0206 0.107 -0.0003 0.0608 -0.1156 0.0452 -0.0179 -0.022 0.0694 -0.0365 0.0531 -46.461 46.8481 2.2747 14 7.877 0.9087 -1.4245 0.5236 -0.913 1.776 0.1886 -0.4274 -0.0587 -0.0218 -0.1689 -0.0376 -0.0951 0.2904 -0.0198 0.1812 -0.0105 -0.0122 0.0786 0.0269 0.1382 -39.2046 34.3181 3.3578 15 3.9514 -1.4928 2.7465 0.6144 -0.9507 6.7309 0.0961 0.0271 -0.1358 -0.1268 0.0195 -0.0139 0.1118 0.4268 -0.1156 0.2141 -0.0018 0.0646 0.0949 -0.0581 0.1826 -42.2886 30.2929 -12.9004 16 5.9248 -0.3856 7.7107 8.9313 1.712 11.6068 -0.0001 0.4946 0.0135 -0.4034 -0.287 -0.167 0.1428 0.3157 0.2871 0.1904 -0.0158 0.0205 0.1514 -0.0632 0.1702 -55.3213 32.378 -19.4708 17 2.8504 0.5984 0.2966 3.4028 1.2478 2.8455 -0.0829 0.2582 0.0632 -0.3253 0.1044 0.1126 0.1129 0.0717 -0.0215 0.098 0.0118 -0.045 0.0395 0.0031 0.0454 -59.1764 37.5492 -14.4353 18 6.9494 5.9031 -2.8904 6.04 0.282 8.5245 -0.1127 -0.0256 0.1068 -0.2478 0.0362 0.133 -0.3142 0.1138 0.0765 0.161 0.027 -0.0413 0.1227 0.0046 0.1021 -59.4073 43.7932 -20.5355 19 3.6368 0.6556 0.9697 1.6788 1.1172 2.2292 0.07 -0.0891 0.0065 -0.0959 -0.0126 0.1143 -0.0233 -0.0088 -0.0574 0.0528 0.0072 -0.0207 0.0079 0.011 0.0772 -61.6867 41.5062 -6.7818 20 12.5633 3.583 -4.0022 4.9628 -4.6417 4.3852 -0.1382 -0.0756 -0.3798 -0.2254 0.2874 0.2206 0.2099 -0.2484 -0.1492 0.203 -0.0136 -0.0153 0.0909 0.0059 0.2458 -73.3092 30.2331 -4.6851 21 2.1314 5.1321 0.7824 12.9442 0.2528 4.9039 -0.1237 -0.0587 -0.1225 -0.2978 -0.0621 -0.3571 -0.2182 -0.2083 0.1858 0.1308 0.0042 -0.0347 0.2573 0.0134 0.168 -29.1215 15.7401 -37.5653 22 3.8297 -3.6825 -0.9451 6.7829 5.6964 8.0999 0.333 0.2465 -0.0225 -0.3764 -0.0963 -0.1096 -0.5761 -0.1717 -0.2367 0.2841 0.0929 -0.0383 0.3129 0.0156 0.2388 -37.7057 26.8039 -27.9413 23 2.2054 0.0904 -0.0967 1.8967 1.4756 4.0136 -0.0014 0.2343 -0.0093 -0.3943 -0.0779 0.4057 0.0656 -0.3346 0.0793 0.1418 0.0322 -0.1194 0.2751 0.0113 0.1589 -32.7748 11.886 -29.2946 24 2.0499 0.3261 -0.514 3.7646 0.5431 1.4582 -0.0804 0.3285 0.0367 -0.1896 0.1004 0.0483 0.0779 -0.2735 -0.02 0.0872 0.0334 -0.0481 0.1821 0.0098 0.0684 -25.1681 14.9071 -28.4251 25 0.1505 0.9761 -1.0409 6.4804 -6.9398 7.4999 0.0658 0.1194 0.0887 0.5202 0.6235 0.5102 -0.6491 -0.5462 -0.6893 0.3062 -0.051 0.1366 0.4313 -0.1396 0.5038 -26.5546 33.2998 -25.8488 26 1.5128 0.322 0.5949 3.2854 -0.0206 0.9067 -0.0952 0.2056 0.0732 -0.1517 0.0575 0.4079 -0.0919 -0.3232 0.0377 0.046 0.033 -0.0357 0.2765 -0.0196 0.179 -35.3395 17.4288 -20.5283 27 6.6212 0.6137 -1.2039 2.0768 0.0988 1.3801 0.1118 0.0016 0.1435 0.1262 -0.0443 0.2597 -0.0623 -0.3553 -0.0675 0.0514 0.0464 -0.0226 0.1347 -0.0187 0.0814 -30.1279 14.8718 -13.4951 28 6.2174 2.4063 -1.9733 2.0893 -0.3701 0.7605 -0.1352 0.1553 -0.1847 -0.1282 0.0159 0.0918 0.0186 -0.058 0.1193 0.0334 0.0222 -0.0424 0.1454 0.0039 0.0976 -26.3022 9.6798 -15.0043 29 3.351 5.1285 -2.9336 9.9383 -6.289 4.1363 -0.0373 -0.1321 -0.0468 0.2078 -0.0441 -0.1484 -0.2328 0.017 0.0814 0.1582 -0.0066 0.0144 0.1182 -0.062 0.1359 -11.5105 23.7492 -8.4857 30 4.635 0.7875 3.0196 3.7833 1.479 6.8776 0.0641 0.0033 0.396 -0.2031 -0.1098 -0.3222 -0.4114 0.2224 0.0457 0.2564 0.0234 0.0384 0.0608 0.0118 0.2088 -11.3647 34.1721 -18.1094 31 2.8559 -0.8483 -1.5458 1.5104 0.7054 5.2696 -0.0281 -0.04 -0.0041 -0.125 -0.076 0.0024 -0.215 -0.1797 0.1041 0.034 0.0049 -0.0026 0.0408 0.0169 0.0689 -6.8044 17.932 -23.7578 32 6.3901 -6.3851 0.3818 6.4069 -0.4011 0.0884 0.1788 0.1694 0.2065 -0.1939 -0.1368 -0.1476 -0.0653 -0.0222 -0.042 0.1601 0.0167 -0.0114 0.1216 0.0661 0.1406 -11.6625 21.268 -29.8292 33 0.7106 -0.5913 0.9937 0.7212 -0.6197 1.617 -0.163 0.0335 0.1689 0.1042 -0.0508 -0.1501 -0.4022 -0.0482 0.2138 0.2664 0.1207 0.0266 0.0851 0.0207 0.2607 -19.8099 31.4142 -20.0041 34 0.9057 -1.7707 -0.151 5.8746 -1.7347 3.8038 0.1467 -0.1061 0.1562 0.2178 0.3424 0.4157 -0.5145 -0.0067 -0.4891 0.1807 0.0737 0.1291 0.1203 -0.0164 0.2772 -22.737 23.7537 -7.1842 35 5.6695 1.3645 1.4503 4.777 -1.7577 5.6073 0.0786 -0.1172 0.2429 0.2648 -0.0886 0.0003 -0.167 -0.3902 0.01 0.0817 0.0537 0.0142 0.1321 -0.0188 0.0891 -29.3317 12.689 -4.0188 36 3.6304 -0.9399 -2.0267 1.9135 -0.2057 2.4387 -0.0182 -0.1863 -0.1712 0.0166 -0.086 -0.1054 -0.0709 -0.0808 0.1042 0.0381 0.0248 -0.0164 0.0815 0.0308 0.0378 -18.471 7.4745 -11.666 37 4.81 2.5827 -3.8403 4.979 -3.179 6.8159 -0.0032 -0.1242 -0.1773 -0.0336 -0.1525 -0.122 0.1909 0.1537 0.1556 0.0914 0.0367 -0.0387 0.0859 -0.0113 0.0977 -13.7625 7.1047 -3.9727 38 8.0883 -0.6666 -3.5953 2.8033 1.5156 2.7209 0.1876 -0.2848 0.1947 0.4573 0.0051 -0.0672 -0.0433 0.0392 -0.1926 0.1392 0.0236 0.0116 0.1243 0.03 0.0619 -20.8702 3.4625 -5.7351 39 1.7801 0.582 0.5635 1.0208 0.3728 0.28 0.0101 -0.1141 -0.3991 -0.2605 0.0907 -0.2092 -0.0837 -0.0708 -0.1008 0.0935 -0.0116 0.0079 0.0911 -0.0252 0.1202 -15.3229 6.575 -22.9766 40 1.1694 -1.1261 2.4777 6.4477 -1.4018 5.4837 0.1536 -0.1295 -0.2226 0.0303 0.1821 0.5543 0.4162 -0.3458 -0.3357 0.1359 -0.0521 0.0059 0.2494 -0.0736 0.2329 -30.6184 -2.0092 -20.1934
Refinement TLS group Show large table (5 x 40) Hide large table ID Refine-ID Refine TLS-ID Selection Selection details 1 X-RAY DIFFRACTION 1 ALL{ AAA|3-8 } 2 X-RAY DIFFRACTION 2 ALL{ AAA|9-16 } 3 X-RAY DIFFRACTION 3 ALL{ AAA|17-21 } 4 X-RAY DIFFRACTION 4 ALL{ AAA|22-26 } 5 X-RAY DIFFRACTION 5 ALL{ AAA|27-46 } 6 X-RAY DIFFRACTION 6 ALL{ AAA|47-60 } 7 X-RAY DIFFRACTION 7 ALL{ AAA|61-73 } 8 X-RAY DIFFRACTION 8 ALL{ AAA|74-83 } 9 X-RAY DIFFRACTION 9 ALL{ AAA|84-93 } 10 X-RAY DIFFRACTION 10 ALL{ AAA|94-135 } 11 X-RAY DIFFRACTION 11 ALL{ AAA|136-147 } 12 X-RAY DIFFRACTION 12 ALL{ AAA|148-156 } 13 X-RAY DIFFRACTION 13 ALL{ AAA|157-174 } 14 X-RAY DIFFRACTION 14 ALL{ AAA|175-184 } 15 X-RAY DIFFRACTION 15 ALL{ AAA|185-201 } 16 X-RAY DIFFRACTION 16 ALL{ AAA|202-207 } 17 X-RAY DIFFRACTION 17 ALL{ AAA|208-227 } 18 X-RAY DIFFRACTION 18 ALL{ AAA|228-235 } 19 X-RAY DIFFRACTION 19 ALL{ AAA|236-267 } 20 X-RAY DIFFRACTION 20 ALL{ AAA|268-275 } 21 X-RAY DIFFRACTION 21 ALL{ BBB|3-7 } 22 X-RAY DIFFRACTION 22 ALL{ BBB|8-14 } 23 X-RAY DIFFRACTION 23 ALL{ BBB|15-33 } 24 X-RAY DIFFRACTION 24 ALL{ BBB|34-66 } 25 X-RAY DIFFRACTION 25 ALL{ BBB|67-73 } 26 X-RAY DIFFRACTION 26 ALL{ BBB|74-98 } 27 X-RAY DIFFRACTION 27 ALL{ BBB|99-117 } 28 X-RAY DIFFRACTION 28 ALL{ BBB|118-128 } 29 X-RAY DIFFRACTION 29 ALL{ BBB|129-142 } 30 X-RAY DIFFRACTION 30 ALL{ BBB|143-153 } 31 X-RAY DIFFRACTION 31 ALL{ BBB|154-168 } 32 X-RAY DIFFRACTION 32 ALL{ BBB|169-179 } 33 X-RAY DIFFRACTION 33 ALL{ BBB|180-190 } 34 X-RAY DIFFRACTION 34 ALL{ BBB|191-202 } 35 X-RAY DIFFRACTION 35 ALL{ BBB|203-211 } 36 X-RAY DIFFRACTION 36 ALL{ BBB|212-225 } 37 X-RAY DIFFRACTION 37 ALL{ BBB|226-235 } 38 X-RAY DIFFRACTION 38 ALL{ BBB|236-245 } 39 X-RAY DIFFRACTION 39 ALL{ BBB|246-265 } 40 X-RAY DIFFRACTION 40 ALL{ BBB|266-275 }