Software Name Version Classification NB d*TREK8.0SSIdata scalingShow REFMAC5.2.0019refinementShow PDB_EXTRACT3.006 data extractionShow CrystalCleardata collection d*TREKdata reduction PHASERphasing
Refinement Starting model : 1s9uResolution : 2.01→30.75 Å / Cor.coef. Fo :Fc : 0.958 / Cor.coef. Fo :Fc free : 0.939 / Occupancy max : 1 / Occupancy min : 0.5 / SU B : 6.515 / SU ML : 0.094 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.13 / ESU R Free : 0.127 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.213 2463 5.1 % RANDOM Rwork 0.178 - - - all 0.236 49796 - - obs 0.18 48639 97.7 % -
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 : 81.39 Å2 / Biso mean : 22.692 Å2 / Biso min : 9.11 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.43 Å2 0.22 Å2 0 Å2 2- - 0.43 Å2 0 Å2 3- - - -0.65 Å2
Refinement step Cycle : LAST / Resolution : 2.01→30.75 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 3345 0 75 411 3831
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_d0.007 0.022 3549 X-RAY DIFFRACTION r_angle_refined_deg1.036 1.945 4844 X-RAY DIFFRACTION r_dihedral_angle_1_deg4.644 5 416 X-RAY DIFFRACTION r_dihedral_angle_2_deg31.863 23.626 171 X-RAY DIFFRACTION r_dihedral_angle_3_deg12.736 15 532 X-RAY DIFFRACTION r_dihedral_angle_4_deg18.4 15 22 X-RAY DIFFRACTION r_chiral_restr0.073 0.2 506 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.02 2754 X-RAY DIFFRACTION r_nbd_refined0.208 0.3 1676 X-RAY DIFFRACTION r_nbtor_refined0.316 0.5 2444 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.196 0.5 510 X-RAY DIFFRACTION r_symmetry_vdw_refined0.231 0.3 59 X-RAY DIFFRACTION r_symmetry_hbond_refined0.244 0.5 35 X-RAY DIFFRACTION r_mcbond_it0.312 1.5 2103 X-RAY DIFFRACTION r_mcangle_it0.554 2 3379 X-RAY DIFFRACTION r_scbond_it1.02 3 1564 X-RAY DIFFRACTION r_scangle_it1.583 4.5 1465
LS refinement shell Resolution : 2.009→2.061 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.312 164 - Rwork 0.27 3339 - all - 3503 - obs - - 95.76 %
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 7.197 -3.0861 2.2302 11.2887 -2.1159 7.1958 -0.2079 -0.9887 0.0075 0.7835 0.4343 0.4245 -0.2762 -0.3482 -0.2264 0.0205 -0.0246 0.0111 0.1155 -0.0235 -0.0052 -50.1261 49.8137 38.9502 2 2.4616 0.9819 -2.7926 1.0358 1.0007 10.1107 -0.1247 -0.1631 0.1293 -0.0795 0.2083 -0.1965 -0.2752 0.9779 -0.0836 -0.0616 -0.027 -0.0165 0.1291 0.0111 0.0432 -40.5794 42.9732 23.4825 3 5.2237 3.0444 -5.4075 2.0523 -1.9612 10.6943 0.0553 -0.376 -0.0844 0.2416 0.1181 -0.2096 0.4837 0.9724 -0.1733 0.004 0.071 -0.0694 0.2757 -0.0194 0.0117 -36.2997 36.044 29.534 4 3.7996 -1.6702 -2.1787 7.6549 0.8946 11.183 0.32 -0.1887 -0.6145 0.3865 -0.1702 0.1783 0.6591 0.3947 -0.1499 -0.0298 0.027 -0.0823 0.0535 0.0516 0.0526 -46.1478 31.8813 35.1367 5 1.835 1.8857 4.3802 10.0353 6.3612 12.834 -0.0671 0.956 -0.6542 0.2384 0.9738 -0.7685 1.7623 2.2033 -0.9067 0.2446 0.2736 -0.0881 0.2961 -0.1042 0.1631 -38.72 25.8754 24.5921 6 7.4172 -1.5382 3.6619 2.1948 -2.4135 6.3372 0.0078 0.0925 -0.1804 -0.0365 -0.0593 -0.125 0.4234 0.7025 0.0515 -0.0248 0.0363 0.0145 0.0671 -0.036 0.0107 -41.2663 34.1658 11.105 7 2.3516 -0.1011 -0.1719 2.0271 -1.124 1.3868 -0.0638 0.1406 0.0102 -0.0622 0.0695 -0.0101 0.0976 0.056 -0.0058 -0.0579 -0.0062 0.0072 -0.0278 0.0098 -0.0476 -54.7702 44.1775 12.5488 8 22.0255 6.1958 -9.6048 4.8255 -1.1916 6.7421 -0.1434 1.3667 -0.1309 -0.4634 0.1395 0.0711 0.3168 -0.2722 0.0039 -0.0424 -0.0101 -0.0083 0.0005 0.0308 -0.0307 -60.016 48.2643 6.7519 9 1.6021 0.2311 -0.4987 0.4857 -0.8928 1.6448 -0.0731 0.058 0.2724 0.1567 -0.0264 0.0441 -0.4593 0.0463 0.0995 -0.0002 -0.0133 0.0044 -0.0262 0.0183 0.0113 -54.8433 57.5632 15.5296 10 12.2422 -1.9196 -1.0392 24.813 10.3894 38.5178 -0.1042 0.4216 1.8238 0.929 -0.1862 -0.113 -1.313 -0.871 0.2905 0.1464 -0.0603 -0.0339 0.0392 0.0107 0.1952 -51.8673 64.6125 22.6129 11 18.2137 -6.5129 -11.6272 3.8232 13.1484 61.5141 0.5134 0.4563 1.202 -0.9758 -1.4005 0.3031 -0.3188 1.4914 0.8871 0.1796 -0.1576 0.0428 0.2389 0.1005 0.4563 -41.9989 56.8293 18.2568 12 21.0836 -3.0272 -17.76 0.8207 6.0153 46.0656 0.4333 -0.5285 0.6077 0.3326 0.1404 -0.6556 -1.249 1.3869 -0.5736 -0.0176 -0.0779 0.0088 -0.0156 0.0113 0.1263 -44.6955 53.6498 10.6614 13 1.2838 -0.1336 1.419 0.0139 -0.1477 1.5684 -0.084 -0.1346 0.0453 -0.1356 -0.0679 -0.0193 -0.343 0.3347 0.152 -0.0733 -0.0432 0.0011 0.0218 -0.0132 0.0239 -46.9667 50.9405 24.0499 14 19.8711 0.349 -1.8635 4.0022 3.4211 5.6111 -0.3418 -0.4449 0.3353 0.1166 0.1833 -0.2521 -0.3057 0.1509 0.1586 0.0386 -0.0278 -0.023 -0.0046 -0.0247 0.024 -48.1662 58.0845 34.0076 15 11.5212 -6.6366 -0.756 11.2121 8.7707 10.7495 -0.1369 0.0124 0.7685 0.0571 -0.1327 -0.0535 -0.3587 0.2088 0.2695 -0.0438 -0.0333 0.0015 -0.0502 -0.0064 0.0273 -54.6075 55.7576 29.452 16 2.1934 -1.1855 -0.1625 2.3756 0.8145 2.1549 0.061 0.0934 -0.1269 -0.0104 -0.0311 0.0665 0.1041 0.0822 -0.03 -0.0776 -0.007 -0.0034 -0.0279 0.0087 -0.0446 -53.6316 39.421 20.4491 17 18.1967 -8.9245 -5.0032 8.6004 -0.1746 15.5837 0.2552 0.2138 -0.9688 -0.3835 -0.2505 0.464 0.7555 0.143 -0.0047 0.0116 0.0311 -0.0742 -0.0142 -0.0069 -0.0078 -45.8868 32.4363 22.1261 18 12.1309 -0.8891 -2.2084 0.1972 1.3357 10.8376 0.477 0.1417 -0.899 -0.0849 -0.1774 0.428 0.7189 0.0293 -0.2995 -0.0183 0.0098 -0.0698 0.0265 0.0188 0.0413 -51.697 34.9758 27.8969 19 4.0352 -3.1395 -1.5533 2.4533 1.2163 0.6036 -0.151 -0.5039 0.2118 0.1699 0.1709 0.0581 -0.0169 0.0489 -0.0199 -0.051 -0.0317 0.0006 0.0304 0.0141 0.0115 -55.1631 42.6943 32.3985 20 1.7967 1.0909 3.2118 2.2683 2.4517 10.7053 -0.0532 -0.1619 0.0029 -0.0935 0.0124 -0.0425 -0.2287 0.1869 0.0407 -0.1106 -0.0133 0.0379 0.0087 0.0132 -0.0212 -62.7615 47.5262 23.5641 21 8.764 -2.0557 2.947 18.0486 17.1858 26.9463 -0.9734 0.6958 -1.6146 0.7677 1.6504 -0.8608 0.2835 -1.1195 -0.6771 0.2123 0.1105 0.0587 0.314 -0.0822 0.0507 -3.8746 83.685 35.5261 22 2.4956 0.3731 -3.6281 7.8028 -6.6118 15.0565 0.3241 -0.5188 0.1747 0.2466 -0.0702 -0.2651 -0.0294 0.3021 -0.2539 -0.0717 -0.011 0.03 -0.0516 -0.0105 -0.0032 -11.7181 72.3128 32.5341 23 3.168 3.0024 -0.3574 6.1579 0.1635 1.8171 -0.0519 0.091 0.0198 -0.4238 0.0258 0.0724 0.1641 -0.2503 0.0261 -0.0498 -0.0231 -0.0191 -0.0007 0.003 -0.058 -15.5068 59.1383 29.7596 24 6.8842 0.1009 2.0288 3.0683 1.6863 4.5823 0.1024 0.3879 -0.3452 -0.3783 0.0363 -0.2262 0.3163 -0.0139 -0.1387 0.1065 -0.0491 0.0168 -0.0232 -0.0003 0.036 -13.2633 47.9363 26.3743 25 4.9556 2.121 0.3095 4.9178 -2.081 1.2411 0.0531 0.0768 -0.2276 -0.1997 0.0098 -0.2547 0.4055 0.0055 -0.0629 -0.0253 -0.0036 -0.0208 -0.0441 -0.0106 -0.0111 -4.5115 54.3633 36.296 26 9.624 1.1698 -5.5602 3.5586 -5.4081 9.7674 -0.2624 -0.2227 -1.3763 -0.384 -0.3956 -0.1785 1.4388 0.0918 0.658 0.3172 -0.0178 -0.0227 -0.0115 0.0191 0.2195 -9.3712 40.6154 35.424 27 6.8271 0.7706 0.3882 0.7723 3.54 17.8569 0.0807 -0.5021 -0.7951 0.4827 -0.0509 -0.5576 1.4713 -0.3896 -0.0297 0.3609 -0.1925 -0.0455 0.0174 0.0339 0.2381 -20.2699 36.8455 32.4087 28 24.3842 2.5299 3.9756 1.3076 -1.4757 4.0594 0.4168 0.1775 -0.4781 -0.4732 0.1118 0.4002 0.9238 -0.4937 -0.5286 0.1737 -0.1942 -0.0383 0.2567 0.0056 0.1181 -29.78 43.1972 34.1814 29 3.0274 -1.6408 1.4264 2.3285 0.4221 3.9458 0.2259 -0.317 -0.1451 0.0703 -0.2851 0.5431 0.1897 -0.4311 0.0592 -0.0386 -0.1564 0.0399 0.198 0.0197 0.0766 -33.2616 55.3262 42.3072 30 4.4486 4.141 -1.8854 10.6789 -2.972 14.1116 0.5286 -0.8207 0.1144 0.7381 -0.5052 0.6805 0.4614 -0.5212 -0.0234 -0.0456 -0.1059 0.0344 0.2892 -0.0474 0.1054 -39.0679 58.9891 39.985 31 11.6258 8.9414 -5.2058 15.8594 -7.7443 5.4577 0.0495 0.3694 0.5002 -0.0937 0.2546 1.1769 -0.077 -0.9772 -0.3041 -0.0498 -0.0201 0.0143 0.1887 -0.0489 0.0395 -34.0962 68.7278 34.4916 32 14.7069 -2.1471 3.0519 42.5704 -5.3309 25.4253 0.0284 0.468 1.4019 -0.6931 -0.0315 1.1307 -1.0776 -1.5327 0.0031 0.0019 0.0717 0.032 0.1946 0.0156 0.1709 -31.4928 73.7903 28.6741 33 17.7062 29.9322 0.905 52.9298 3.9876 12.6117 -0.7174 -0.4738 0.5694 -1.4871 0.1975 2.3814 -0.132 -2.0287 0.5199 0.0952 -0.0586 -0.1261 0.3976 -0.0431 0.1192 -30.1338 62.5233 23.4495 34 3.0766 2.5799 -2.6563 3.4197 -1.8043 2.436 -0.0671 0.2554 0.117 -0.087 0.0915 0.1915 0.1236 -0.503 -0.0244 -0.05 -0.0291 -0.0042 0.1102 0.0102 0.001 -26.148 62.3821 28.5109 35 10.1367 2.4996 -9.5969 7.1911 -2.0371 9.1023 0.0138 0.2274 0.021 -0.2768 0.0653 0.3105 -0.3241 -0.7764 -0.0791 -0.0216 0.007 -0.0114 0.0405 0.0031 0.0542 -20.1795 74.4524 30.4135 36 1.6076 -0.5078 -0.6941 5.4641 0.559 1.1708 0.1239 -0.2238 -0.0336 0.3724 -0.2252 0.1031 0.108 -0.2418 0.1013 -0.06 -0.0931 -0.0046 0.0795 0.0052 -0.0193 -23.1593 60.0432 41.7444 37 9.6866 -15.437 -2.3828 32.9683 11.4724 7.6263 -1.4668 -0.794 -1.4101 0.1024 0.4724 1.7228 1.7374 0.0621 0.9944 0.1328 -0.1264 -0.0163 0.0278 0.0454 0.105 -19.8913 41.7468 40.7042 38 6.6338 5.8067 1.9395 24.6489 7.2423 4.5068 0.1452 -0.7653 -0.5283 0.9934 -0.0553 0.0431 0.7192 0.0992 -0.0899 0.0356 -0.0777 -0.0137 0.0638 0.0579 0.0094 -15.6533 47.4914 37.8809 39 2.9837 0.2294 0.2928 10.4743 0.2215 2.0291 0.0331 -0.1219 0.1892 0.5819 0.1334 -0.024 -0.0299 -0.0317 -0.1665 -0.0745 -0.0574 0.008 0.0074 0.0069 -0.0307 -13.8874 64.0565 40.7099 40 11.9041 8.9521 -8.5195 12.1877 -9.8604 8.2835 0.6782 -0.8347 0.3423 0.5051 -0.521 0.514 -0.1567 -0.1795 -0.1573 0.0095 -0.1174 0.0311 0.2082 -0.0559 -0.0083 -28.9663 63.5468 47.8582
Refinement TLS group Show large table (5 x 40) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A1 - 11 2 X-RAY DIFFRACTION 2 A12 - 26 3 X-RAY DIFFRACTION 3 A27 - 44 4 X-RAY DIFFRACTION 4 A45 - 59 5 X-RAY DIFFRACTION 5 A60 - 64 6 X-RAY DIFFRACTION 6 A65 - 82 7 X-RAY DIFFRACTION 7 A83 - 93 8 X-RAY DIFFRACTION 8 A94 - 98 9 X-RAY DIFFRACTION 9 A99 - 110 10 X-RAY DIFFRACTION 10 A111 - 115 11 X-RAY DIFFRACTION 11 A116 - 120 12 X-RAY DIFFRACTION 12 A121 - 125 13 X-RAY DIFFRACTION 13 A126 - 139 14 X-RAY DIFFRACTION 14 A140 - 145 15 X-RAY DIFFRACTION 15 A146 - 150 16 X-RAY DIFFRACTION 16 A151 - 174 17 X-RAY DIFFRACTION 17 A175 - 179 18 X-RAY DIFFRACTION 18 A180 - 184 19 X-RAY DIFFRACTION 19 A185 - 191 20 X-RAY DIFFRACTION 20 A192 - 204 21 X-RAY DIFFRACTION 21 B-3 - 1 22 X-RAY DIFFRACTION 22 B2 - 6 23 X-RAY DIFFRACTION 23 B7 - 22 24 X-RAY DIFFRACTION 24 B23 - 43 25 X-RAY DIFFRACTION 25 B44 - 57 26 X-RAY DIFFRACTION 26 B58 - 64 27 X-RAY DIFFRACTION 27 B65 - 71 28 X-RAY DIFFRACTION 28 B72 - 80 29 X-RAY DIFFRACTION 29 B81 - 94 30 X-RAY DIFFRACTION 30 B95 - 101 31 X-RAY DIFFRACTION 31 B102 - 109 32 X-RAY DIFFRACTION 32 B110 - 115 33 X-RAY DIFFRACTION 33 B116 - 120 34 X-RAY DIFFRACTION 34 B121 - 142 35 X-RAY DIFFRACTION 35 B143 - 147 36 X-RAY DIFFRACTION 36 B148 - 168 37 X-RAY DIFFRACTION 37 B169 - 173 38 X-RAY DIFFRACTION 38 B174 - 180 39 X-RAY DIFFRACTION 39 B181 - 195 40 X-RAY DIFFRACTION 40 B196 - 204