Software Name Version Classification SBC-Collectdata collection HKL-3000phasing REFMAC5.5.0102refinement HKL-3000data reduction HKL-3000data scaling
Refinement Method to determine structure : SAD / Resolution : 1.55→40 Å / Cor.coef. Fo :Fc : 0.976 / Cor.coef. Fo :Fc free : 0.969 / SU B : 2.597 / SU ML : 0.042 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 2 / ESU R : 0.067 / ESU R Free : 0.067 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.169 4956 5 % RANDOM Rwork 0.144 - - - obs 0.145 94110 99.5 % - all - 99100 - -
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 : 8.85 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.32 Å2 0 Å2 -1.05 Å2 2- - -0.08 Å2 0 Å2 3- - - -0.32 Å2
Refinement step Cycle : LAST / Resolution : 1.55→40 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 5109 0 23 880 6012
Refine LS restraints Show large table (5 x 33) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.016 0.022 5264 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 3560 X-RAY DIFFRACTION r_angle_refined_deg1.509 1.963 7153 X-RAY DIFFRACTION r_angle_other_deg0.935 3 8687 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.078 5 652 X-RAY DIFFRACTION r_dihedral_angle_2_deg38.193 24.286 245 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.469 15 880 X-RAY DIFFRACTION r_dihedral_angle_4_deg16.853 15 30 X-RAY DIFFRACTION r_chiral_restr0.093 0.2 791 X-RAY DIFFRACTION r_gen_planes_refined0.007 0.021 5851 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 1071 X-RAY DIFFRACTION r_nbd_refinedX-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refinedX-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refinedX-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refinedX-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refinedX-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it0.774 1.5 3229 X-RAY DIFFRACTION r_mcbond_other0.247 1.5 1307 X-RAY DIFFRACTION r_mcangle_it1.39 2 5223 X-RAY DIFFRACTION r_scbond_it2.368 3 2035 X-RAY DIFFRACTION r_scangle_it3.666 4.5 1925 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
LS refinement shell Resolution : 1.55→1.59 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.293 350 - Rwork 0.283 6787 - obs - - 97.73 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 36) 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 0.205 0.2587 -0.1009 1.7003 -0.7473 4.2172 0.0227 0.1058 -0.0586 -0.0013 -0.0981 0.0913 -0.0002 -0.1863 0.0754 0.0596 0.0118 -0.0098 0.1157 -0.0298 0.0913 17.09 62.2819 -3.2916 2 0.5004 0.149 -0.9142 1.9873 -0.5642 5.6258 0.0038 0.1894 -0.19 -0.0691 -0.0896 0.2254 0.1164 -0.4835 0.0858 0.0527 -0.0221 -0.0357 0.1675 -0.0805 0.1207 12.0229 56.5844 -7.0006 3 0.9386 -0.3545 0.4203 0.5372 -0.1086 1.7284 0.0802 0.1238 -0.1328 -0.0627 -0.0423 0.0295 0.0797 -0.0575 -0.0379 0.0908 0.0012 -0.0071 0.1081 -0.0286 0.088 23.651 59.3094 -6.2526 4 6.3053 1.9434 2.0431 2.3962 1.785 3.2769 -0.0041 0.0859 -0.241 0.0899 -0.1 0.0597 0.2478 -0.0713 0.1041 0.1033 -0.0235 -0.0094 0.0873 -0.0644 0.0965 21.1101 50.9092 -3.7953 5 0.8361 -0.0857 0.9902 0.1951 0.09 1.3545 0.037 0.1988 -0.0377 -0.0171 -0.0062 0.0038 -0.0238 0.2117 -0.0307 0.0799 0.0014 0.0093 0.1215 -0.0188 0.067 39.6844 61.2441 2.4251 6 1.8726 -0.0592 -0.044 1.0384 0.3817 0.4708 0.0468 0.0451 -0.1126 0.1302 0.0324 -0.0409 0.1019 0.0506 -0.0792 0.113 0 -0.0069 0.0661 -0.0063 0.0873 44.425 57.9878 24.6578 7 6.4012 -1.2466 -3.7584 2.0442 1.5059 8.1434 -0.2547 -0.0597 -0.5239 0.1694 0.0369 0.0823 0.3165 0.3607 0.2178 0.0917 0.0036 0.0072 0.0349 -0.0046 0.1482 39.428 48.1969 20.1256 8 3.6149 2.587 0.331 2.9288 0.317 0.6996 0.0124 0.2491 -0.1886 0.0224 0.1063 -0.1616 0.0367 0.1715 -0.1186 0.063 -0.0027 -0.0021 0.1152 -0.0415 0.0832 51.2425 57.2768 12.751 9 0.4484 -0.0705 0.2736 0.3863 -0.0737 0.6786 -0.0193 0.0788 0.0013 0.0217 0.0154 0.0153 -0.0179 0.0386 0.0039 0.0837 -0.0174 0.0043 0.0722 -0.0027 0.0846 40.4841 66.3823 15.3683 10 2.9313 -1.3409 0.5967 3.7223 2.36 1.7878 -0.1054 0.1741 0.2124 -0.0846 0.0858 -0.1637 -0.1401 0.1246 0.0197 0.0672 -0.0317 -0.0134 0.0715 -0.0013 0.0755 52.4563 73.0448 19.0333 11 1.562 0.9129 1.1582 1.8169 0.8115 1.6752 -0.0257 0.1995 0.14 -0.0219 -0.0493 -0.042 -0.0516 0.1258 0.075 0.093 -0.0259 -0.0106 0.078 0.0306 0.0777 41.5485 75.2739 11.1327 12 1.1718 0.2791 0.2571 0.2728 0.0782 0.5865 -0.0622 0.0667 0.0663 -0.0127 0.018 0.0103 -0.0639 -0.0073 0.0442 0.1006 -0.0127 0 0.0539 0.0093 0.0856 29.5943 72.2566 14.952 13 0.4102 -0.3112 0.1245 1.9197 1.1869 2.1271 0.0658 0.1523 0.0441 -0.1402 -0.1096 -0.049 -0.1726 0.1072 0.0438 0.084 0.0128 0.0062 0.1058 0.0132 0.0616 28.685 70.7929 -7.9418 14 1.8823 -2.438 -0.1397 14.9631 3.4714 3.0824 0.0806 0.3542 0.0525 -0.8327 0.0364 0.0322 0.0645 0.4037 -0.117 0.16 0.0482 -0.0037 0.1813 -0.0029 0.0126 25.4308 67.9025 -19.6972 15 0.4796 0.1876 -0.4937 0.6817 -0.4334 1.684 0.0603 0.0768 0.0394 -0.0545 -0.0373 0.091 -0.117 -0.1279 -0.023 0.0902 0.0309 0.0022 0.1026 0.0065 0.0756 17.3155 73.1806 -4.016 16 4.074 0.6434 -5.1167 4.4362 -3.3227 19.2965 0.3745 -0.1612 0.41 0.3958 -0.0029 0.1091 -1.538 0.03 -0.3716 0.177 0.0683 0.0287 0.0849 -0.0273 0.1667 10.964 78.19 5.1868 17 0.839 0.4655 1.3345 -0.4458 0.7065 3.336 0.0966 0.1639 -0.0217 0.0521 -0.1116 0.1518 0.0425 -0.5286 0.015 0.0476 0.0347 -0.0216 0.3017 -0.0563 0.2269 6.7424 66.2863 -4.321 18 17.3324 5.4383 24.5128 28.3752 -1.3798 30.9102 -0.8397 0.5109 1.0542 -1.0461 -0.0315 0.9073 -0.6586 0.5609 0.8712 0.0773 0.008 -0.0922 0.3613 0.1543 0.2469 7.0629 70.4973 -13.5575 19 0.8166 -0.4023 0.1774 1.6717 1.3736 4.142 -0.0544 -0.158 -0.0066 -0.0099 0.0245 0.0076 0.0755 0.0401 0.0299 0.0798 0.0273 0.0009 0.0949 0.0002 0.0809 46.5291 66.136 46.6683 20 1.83 -0.3748 0.5901 0.3226 -0.1677 1.327 -0.0334 -0.2835 -0.118 0.015 0.0674 0.0286 0.0529 0.0162 -0.0339 0.0799 0.0326 0.0095 0.1188 0.017 0.0697 48.1357 64.4475 53.405 21 3.0165 -0.3742 1.2721 0.7661 -0.518 1.1079 0.0075 -0.117 -0.3337 0.018 0.0233 -0.0032 0.1975 -0.0121 -0.0309 0.1174 0.0309 0.0158 0.0771 0.0466 0.1179 41.015 55.4617 47.9459 22 0.8031 0.1122 0.5414 0.2511 0.0441 0.5635 -0.0392 -0.1779 -0.068 0.0436 0.0068 0.0181 0.0497 -0.1035 0.0324 0.0933 0.0024 0.0281 0.0992 0.0186 0.0776 25.6593 62.0537 43.4345 23 0.5674 0.0778 0.3539 0.429 0.8294 1.8593 0.0501 -0.1092 -0.1114 0.0318 -0.0003 0.0765 0.058 -0.134 -0.0498 0.1078 -0.0226 0.0288 0.0869 0.0372 0.0995 20.4595 56.0789 36.427 24 3.6269 0.6381 -0.1325 0.7037 -0.5528 0.5691 0.0165 0.1543 -0.117 -0.0542 0.0138 -0.0059 0.1503 -0.0275 -0.0303 0.1346 -0.026 0.008 0.0632 -0.0038 0.1002 21.3971 56.0035 19.1813 25 4.5877 1.4226 -4.7287 3.2908 -1.0711 5.389 -0.1004 -0.0156 -0.2702 -0.038 0.0033 -0.0397 0.2496 -0.0268 0.0971 0.0953 -0.0227 0.002 0.0449 0.0151 0.1249 27.2278 47.9941 27.0622 26 2.6691 1.2029 1.3423 3.1664 -0.8637 1.1559 0.0806 -0.1326 -0.089 0.0877 0.0209 0.0334 0.0421 -0.1641 -0.1015 0.0852 -0.0452 0.0268 0.1143 0.0131 0.1002 11.1864 56.0854 32.1419 27 0.6278 -0.2157 0.0778 0.2127 0.0888 0.6743 -0.0044 -0.0293 -0.0087 0.0082 -0.0047 -0.0088 0.0238 -0.0405 0.0091 0.0848 -0.0086 0.0147 0.0669 0.0028 0.0958 24.2411 64.5795 29.0061 28 1.9053 1.9133 0.8946 5.8492 -1.3909 2.2131 -0.1483 -0.0663 0.1487 -0.0392 0.1839 0.4299 -0.1279 -0.3095 -0.0356 0.063 0.0229 -0.0101 0.109 -0.0048 0.1139 9.8871 69.2397 24.7463 29 0.8002 -0.1351 0.2323 0.3301 0.0762 0.304 -0.0676 -0.0538 0.0926 0.0108 0.0108 0.0223 -0.0316 -0.0221 0.0567 0.0944 0.0085 -0.0008 0.0637 -0.0053 0.0847 29.7522 72.8194 30.0085 30 1.5775 -0.2849 -1.4212 1.848 -0.4785 2.9816 -0.0479 -0.1576 0.0796 0.075 0.0475 0.065 -0.0698 -0.0703 0.0005 0.0786 0.0427 0.004 0.1038 -0.0144 0.0715 32.1999 74.507 47.9322 31 3.4762 -3.2299 -0.6968 10.878 -0.2595 7.5689 -0.1577 -0.5368 -0.0828 0.7771 0.1065 0.2533 -0.3019 -0.354 0.0513 0.1247 0.0688 0.0291 0.2377 0.0267 0.008 34.5601 68.0179 60.0519 32 5.5074 5.6771 -2.8596 19.6255 -9.5791 7.0217 0.2845 -0.8056 0.19 0.718 -0.0531 0.3848 0.0045 0.2362 -0.2313 0.2648 0.0766 -0.015 0.2584 -0.0492 0.0325 39.9402 71.0605 63.2485 33 1.0706 -0.4926 -0.6921 0.5188 0.2359 1.3629 -0.0786 -0.103 0.1421 0.0215 0.0533 -0.036 -0.0882 -0.0119 0.0253 0.089 0.0248 -0.0146 0.0837 -0.0263 0.0902 44.521 77.1882 45.2585 34 3.8647 0.2388 -3.0399 2.2909 1.2147 10.677 0.0927 0.1839 0.5044 -0.1429 0.0275 0.0103 -0.856 -0.3801 -0.1201 0.1161 0.0229 -0.0353 0.0216 -0.0012 0.1468 49.2029 83.1107 39.7896 35 2.3898 0.3491 0.8299 0.6519 -0.3612 0.6879 -0.0484 -0.1759 0.1092 -0.0419 -0.0275 0.0153 0.0208 -0.0171 0.0759 0.0814 0.0293 -0.0233 0.1125 -0.0184 0.0865 55.5813 72.5644 49.3223 36 13.9398 9.0485 7.7944 21.2987 2.7016 10.0716 -0.401 -0.6859 0.7702 0.3458 0.0043 0.3525 -0.4985 -0.2915 0.3967 0.1238 0.0632 -0.0178 0.2493 -0.1407 0.1125 54.5903 78.196 58.2246
Refinement TLS group Show large table (5 x 36) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A12 - 29 2 X-RAY DIFFRACTION 2 A30 - 42 3 X-RAY DIFFRACTION 3 A43 - 62 4 X-RAY DIFFRACTION 4 A63 - 72 5 X-RAY DIFFRACTION 5 A73 - 122 6 X-RAY DIFFRACTION 6 A123 - 134 7 X-RAY DIFFRACTION 7 A135 - 142 8 X-RAY DIFFRACTION 8 A143 - 154 9 X-RAY DIFFRACTION 9 A155 - 181 10 X-RAY DIFFRACTION 10 A182 - 191 11 X-RAY DIFFRACTION 11 A192 - 204 12 X-RAY DIFFRACTION 12 A205 - 244 13 X-RAY DIFFRACTION 13 A245 - 262 14 X-RAY DIFFRACTION 14 A263 - 285 15 X-RAY DIFFRACTION 15 A286 - 322 16 X-RAY DIFFRACTION 16 A323 - 334 17 X-RAY DIFFRACTION 17 A335 - 346 18 X-RAY DIFFRACTION 18 A347 - 352 19 X-RAY DIFFRACTION 19 B13 - 29 20 X-RAY DIFFRACTION 20 B30 - 54 21 X-RAY DIFFRACTION 21 B55 - 74 22 X-RAY DIFFRACTION 22 B75 - 108 23 X-RAY DIFFRACTION 23 B109 - 124 24 X-RAY DIFFRACTION 24 B125 - 134 25 X-RAY DIFFRACTION 25 B135 - 145 26 X-RAY DIFFRACTION 26 B146 - 155 27 X-RAY DIFFRACTION 27 B156 - 180 28 X-RAY DIFFRACTION 28 B181 - 192 29 X-RAY DIFFRACTION 29 B193 - 243 30 X-RAY DIFFRACTION 30 B244 - 256 31 X-RAY DIFFRACTION 31 B257 - 264 32 X-RAY DIFFRACTION 32 B265 - 292 33 X-RAY DIFFRACTION 33 B293 - 322 34 X-RAY DIFFRACTION 34 B323 - 335 35 X-RAY DIFFRACTION 35 B336 - 347 36 X-RAY DIFFRACTION 36 B348 - 352