Software Name Version Classification NB DENZOdata reductionShow SCALEPACKdata scalingShow REFMAC5.6.0117refinementShow PDB_EXTRACT3.11 data extractionShow Blu-Icedata collection BALBESphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB ENTRY 2QCBResolution : 1.5→36.94 Å / Cor.coef. Fo :Fc : 0.947 / Cor.coef. Fo :Fc free : 0.935 / Occupancy max : 1 / Occupancy min : 0.45 / SU B : 2.483 / SU ML : 0.05 / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.095 / ESU R Free : 0.094 / Stereochemistry target values : MAXIMUM LIKELIHOODDetails : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDEDRfactor Num. reflection % reflection Selection details Rfree 0.2299 3343 5 % RANDOM Rwork 0.2006 - - - obs 0.2021 63726 100 % - all - 63726 - -
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 : 93.85 Å2 / Biso mean : 25.9489 Å2 / Biso min : 13.2 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.02 Å2 0 Å2 0 Å2 2- - 0.14 Å2 0 Å2 3- - - -0.12 Å2
Refinement step Cycle : LAST / Resolution : 1.5→36.94 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 3683 0 70 366 4119
Refine LS restraints Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.013 0.02 3878 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 2405 X-RAY DIFFRACTION r_angle_refined_deg1.671 1.912 5300 X-RAY DIFFRACTION r_angle_other_deg1.983 3 5845 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.823 5 489 X-RAY DIFFRACTION r_dihedral_angle_2_deg29.756 23.58 162 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.018 15 520 X-RAY DIFFRACTION r_dihedral_angle_4_deg17.95 15 20 X-RAY DIFFRACTION r_chiral_restr0.124 0.2 591 X-RAY DIFFRACTION r_gen_planes_refined0.008 0.02 4448 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 876
LS refinement shell Resolution : 1.5→1.539 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.229 183 - Rwork 0.207 3698 - all - 3881 - obs - - 72.04 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 48) 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 8.4516 -1.7792 1.3053 0.646 1.2686 9.0604 0.0476 -0.2363 0.2321 -0.0671 0.0797 -0.0937 -0.4008 0.1875 -0.1273 0.1413 -0.0296 -0.0541 0.1856 -0.006 0.1814 42.9706 -1.9729 34.1844 2 4.3452 1.6095 -0.3885 3.1667 -0.5482 0.9963 -0.0749 -0.0329 -0.1107 0.0206 0.0419 -0.1706 -0.0192 -0.0156 0.033 0.0798 -0.0008 -0.0064 0.1299 -0.0276 0.1016 40.7862 -6.7064 31.0137 3 5.2509 3.2928 -2.4287 7.5561 -4.5151 3.9533 -0.0079 -0.2097 -0.2826 0.1608 -0.0619 -0.1046 0.0707 0.0579 0.0697 0.0459 0.0121 0.0025 0.1143 -0.0338 0.0908 41.3087 -11.3296 28.1682 4 17.6898 -0.9526 -6.2402 27.2127 -8.1675 6.3276 -0.1144 -1.305 -0.2224 1.7225 -0.1497 -0.5525 0.395 0.6288 0.2642 0.6488 0.0516 -0.033 0.179 0.0027 0.1167 44.8635 -20.0898 30.5966 5 0.5788 0.1326 0.0973 3.3411 -0.206 0.5275 0.0444 -0.0358 0.0406 0.0842 -0.0779 -0.0728 -0.0176 0.0273 0.0335 0.0234 -0.0073 -0.0042 0.1256 -0.0059 0.1282 41.6851 -4.0358 23.7981 6 8.5929 -2.9117 3.4799 9.878 4.6 5.1662 0.0724 -0.3085 -0.6707 0.2826 0.2274 0.2088 0.2327 -0.034 -0.2998 0.035 -0.0178 0.0118 0.1611 0.0255 0.1951 39.1882 -24.0535 20.856 7 1.3903 0.5707 0.9179 7.4916 1.4271 0.9466 -0.0348 -0.0688 0.0875 0.0455 -0.0214 0.1187 -0.0399 -0.0172 0.0562 0.0085 -0.0178 0.0125 0.1143 -0.0073 0.1219 35.5284 -3.8977 24.6265 8 10.1434 -4.5762 2.7281 11.9431 16.0951 31.579 -0.0918 -0.6613 0.0293 0.3891 -0.0925 0.1331 0.1301 -0.8546 0.1843 0.4561 -0.0209 0.0511 0.2024 -0.0532 0.1531 34.097 3.6452 37.5322 9 0.7939 0.4682 0.3036 1.3622 1.0013 3.8689 -0.0123 0.024 -0.0785 0.015 0.0104 0.0786 -0.0095 -0.0262 0.0019 0.0068 0.0019 -0.0005 0.1203 -0.0069 0.1314 31.2759 -10.8774 20.6671 10 19.3996 -10.0561 -6.6334 12.0195 4.7196 6.9532 0.201 0.9422 -0.3469 -0.5199 -0.2977 0.0274 0.0325 -0.2594 0.0967 0.0956 -0.0065 -0.0207 0.2065 -0.0284 0.1553 24.857 -20.6903 8.0748 11 1.46 0.8246 2.0333 6.5276 5.9773 9.5453 0.0315 -0.0038 -0.0694 0.037 -0.0887 0.203 0.0669 -0.136 0.0572 0.0024 -0.0066 0.0117 0.115 -0.0029 0.1343 26.6323 -13.129 20.2922 12 17.6266 3.7298 7.1574 8.0549 4.9318 13.6284 -0.2293 -0.9446 0.0124 0.44 0.0496 -0.1319 -0.0002 0.1212 0.1797 0.1135 0.0161 0.0064 0.1435 -0.0073 0.1418 36.8566 -4.1189 36.0235 13 4.4673 -1.4039 0.3711 1.2345 -0.1916 1.8014 0.0668 0.128 -0.0296 -0.1276 0.0207 -0.0537 -0.02 0.0512 -0.0875 0.0695 -0.0125 0.0126 0.1414 -0.0218 0.1299 42.6566 -7.565 4.2404 14 2.6298 4.2062 -3.8457 13.7055 -3.3177 6.7771 -0.1211 -0.2632 -0.1931 -0.0102 -0.2008 -0.2938 0.2887 0.4754 0.3219 0.0245 0.0223 0.0194 0.1611 -0.0108 0.1664 48.334 -9.5228 13.0394 15 19.0582 -2.4637 4.1076 11.8745 -4.3614 6.0132 -0.2321 0.353 1.1164 0.1164 0.1478 -0.0681 -0.5228 -0.1472 0.0843 0.1824 -0.0079 0.0064 0.1148 -0.0098 0.1446 38.259 4.1332 6.2989 16 14.6686 1.5723 1.797 18.4486 -2.0706 18.732 0.2471 1.0128 0.8995 -1.7776 -0.1205 -0.3182 -0.804 0.3779 -0.1266 0.2489 0.0082 0.057 0.2179 0.0349 0.2036 45.3827 7.8345 6.7951 17 1.111 -0.4072 -0.1964 2.2866 -0.218 0.8603 0.0582 0.0683 -0.1056 -0.149 -0.0722 -0.0997 0.1521 0.0183 0.014 0.0477 0.0064 0.0046 0.1304 -0.015 0.1226 41.0445 -12.5351 13.0865 18 9.3427 1.0313 -4.9296 20.1527 -6.3497 13.6797 0.0285 0.1784 0.1053 -0.3194 -0.091 -0.1337 -0.4391 0.2978 0.0625 0.039 -0.021 0.011 0.1441 -0.0248 0.1608 45.4082 11.6034 13.3781 19 0.6998 0.0066 -0.2728 1.9603 0.6292 0.8398 -0.05 0.0486 -0.0073 -0.059 0.0112 0.1517 0.0305 0.0161 0.0387 0.0148 0.0065 -0.0033 0.118 -0.0099 0.12 36.9692 -5.5063 11.4492 20 7.9301 -6.951 -13.2721 6.3327 11.7426 22.2641 0.0714 0.8295 -0.2166 -0.2888 -0.478 0.2362 -0.1705 -1.2831 0.4066 0.3654 -0.162 -0.0657 0.3245 0.0039 0.1279 34.9798 -13.1429 1.0226 21 1.1923 -0.1336 0.126 2.8338 3.0719 5.7824 -0.0156 -0.0407 0.1387 0.0811 0.0182 0.0429 0.0091 -0.0369 -0.0026 0.0201 -0.0011 0.0052 0.1058 -0.001 0.1355 30.8457 0.6801 17.4418 22 17.4158 7.9344 2.9586 13.1029 4.8002 6.8705 0.0222 -0.7798 0.3671 0.4078 -0.2007 0.1254 0.0147 -0.195 0.1784 0.0577 0.0029 0.0231 0.1809 -0.0492 0.1726 24.2501 8.1704 27.4803 23 3.8201 -1.671 -2.7515 1.0873 1.6851 3.9704 0.1413 0.2105 0.1027 -0.1808 -0.0613 -0.0289 -0.149 -0.0903 -0.08 0.062 -0.0078 0.0077 0.0873 0.0072 0.1359 34.3358 -3.8552 7.2498 24 2.9066 -2.9014 -3.1762 11.5385 8.6978 7.0065 0.0503 -0.2556 -0.1695 0.3578 0.0257 -0.2751 0.2184 0.1284 -0.076 0.1414 -0.0218 0.0125 0.2528 0.0074 0.2267 45.0225 -17.5995 -1.9176 25 5.8189 -1.495 0.2242 0.4152 -0.4698 5.5518 0.0024 -0.0971 -0.3408 -0.013 0.0423 0.0922 0.3031 -0.0448 -0.0447 0.1301 0.0155 0.0267 0.1842 0.009 0.1821 4.1436 -9.3601 32.4526 26 9.7618 -2.6591 1.5012 2.163 -2.4436 7.6051 0.0043 -0.4865 0.3846 0.4223 0.0391 -0.0274 -0.4806 -0.1975 -0.0434 0.1972 0 0.0328 0.1587 -0.0512 0.1602 14.1709 2.445 32.8901 27 6.4129 6.4584 0.5436 14.1122 2.2176 2.155 -0.1085 -0.1077 0.0815 -0.3166 0.0061 0.1426 -0.1883 -0.2229 0.1024 0.1107 0.0236 0.0153 0.1771 0.0165 0.1293 2.4172 -6.3657 27.3941 28 3.8006 -1.3535 0.3555 1.9931 1.7537 2.6001 -0.1367 -0.0165 0.4711 -0.1223 -0.0505 0.1036 -0.4069 -0.0679 0.1872 0.1733 0.008 0.1064 0.163 -0.0102 0.2653 6.5274 1.7899 25.4887 29 1.0697 -0.5298 0.1972 1.8139 -0.3848 0.3784 -0.02 -0.0844 0.0044 0.2166 0.0448 0.1633 -0.0615 -0.0492 -0.0248 0.0602 0.0054 0.0173 0.1288 -0.0062 0.1316 7.2972 -6.8508 23.9616 30 7.9543 -4.3576 -3.1537 17.091 2.2232 4.4375 0.0571 -0.0558 0.3614 -0.3715 -0.0751 -0.1233 -0.1926 -0.1898 0.018 0.0469 0.0176 -0.0019 0.1275 -0.006 0.2094 4.1951 12.0135 17.774 31 1.3166 -0.2869 0.146 5.3006 -2.7984 2.4478 -0.036 -0.0765 0.0544 0.1911 -0.0116 -0.0638 -0.1001 -0.0218 0.0476 0.0317 -0.0063 0.0043 0.1099 -0.0193 0.1177 12.5386 -3.6962 22.8784 32 7.6588 -0.9134 -1.0925 11.1481 -10.3395 32.0524 -0.2597 -1.0031 0.0556 1.0879 -0.2942 -0.3881 0.4946 0.5062 0.5539 0.2887 -0.0283 0.0068 0.2472 0.0148 0.1475 13.6102 -9.6353 37.5992 33 1.303 0.8066 -0.9743 3.9249 -4.3268 8.7062 -0.0035 0.0309 0.1434 -0.0982 0.0366 -0.0081 0.1565 -0.0536 -0.0331 0.0115 -0.0024 -0.0017 0.1045 -0.0075 0.1397 18.3966 -0.3558 17.736 34 24.9863 -12.2879 6.755 7.1836 -8.1995 22.7617 0.2453 0.9497 0.2085 -0.2771 -0.4789 -0.1301 0.6275 0.3731 0.2337 0.2294 -0.0535 -0.0104 0.1793 0.0515 0.1467 25.2075 5.5598 5.0286 35 2.9507 1.5532 -3.8697 2.8948 -4.0721 12.259 -0.0085 -0.0205 0.0695 0.1267 -0.042 -0.0914 -0.0979 0.0379 0.0505 0.0214 -0.0017 -0.0043 0.0895 -0.0162 0.1451 22.052 0.6107 19.7362 36 2.6174 -2.4276 -0.3162 2.6025 0.412 8.5111 -0.079 -0.5503 -0.1467 0.3206 0.299 0.3997 -0.3613 -0.1679 -0.22 0.2997 -0.0719 0.1324 0.3026 -0.1378 0.2925 7.4869 -5.0094 36.5353 37 10.237 1.515 -0.7552 0.2748 0.4544 6.4632 0.0555 0.1436 0.3262 -0.033 0.0113 0.0526 -0.4013 -0.1078 -0.0669 0.1331 -0.0143 -0.0428 0.1668 0.0186 0.1637 6.3403 -5.355 0.9209 38 5.5493 -2.0913 -0.818 3.0691 1.0014 0.793 0.0096 0.1828 -0.1953 -0.0752 -0.073 0.1131 0.0021 -0.0177 0.0634 0.083 0.007 0.0081 0.1454 -0.003 0.1106 10.5866 -12.1872 3.9949 39 7.0804 0.1489 1.0435 11.9188 1.1498 6.0423 -0.1695 0.0737 0.4232 0.062 0.1414 0.6068 -0.4464 -0.2353 0.0281 0.0509 0.0109 -0.0189 0.1465 -0.0005 0.1667 0.5393 -0.8107 10.3528 40 17.2694 -7.6649 -4.5894 11.0172 5.6713 2.9603 -0.1361 -0.3062 -0.6376 -0.055 0.1276 0.0237 -0.0211 0.088 0.0085 0.0346 -0.0042 0.0077 0.1286 0.004 0.1419 10.5371 -17.9459 7.9407 41 18.4856 -11.2967 -3.7375 19.7532 -2.3197 4.6851 0.2457 1.2748 -0.7099 -1.691 -0.5354 1.0505 1.2894 -0.7247 0.2897 0.4659 -0.1276 0.0228 0.2556 -0.0899 0.2092 4.1122 -22.4655 8.4025 42 1.2403 0.2646 -0.1623 3.4555 -0.3616 0.8106 -0.0234 0.1244 0.1698 -0.2618 0.0256 0.1208 -0.0932 -0.0108 -0.0023 0.0606 0.0064 -0.0198 0.13 0.0016 0.1469 8.72 -1.4409 10.2524 43 12.6198 4.5016 2.6522 20.668 -0.9654 17.3849 0.1342 0.2613 -0.5594 0.0805 -0.0998 0.3126 0.8743 -0.1853 -0.0345 0.0698 -0.0182 -0.0203 0.1345 0.0047 0.1934 4.3811 -25.0125 15.7751 44 1.285 0.7612 -0.1482 4.9225 -2.0883 1.6002 0.0099 0.0074 -0.0072 -0.0436 -0.0557 -0.0027 -0.0181 -0.0099 0.0458 0.0198 0.0137 0.0005 0.106 -0.005 0.1158 12.9932 -10.6215 13.8007 45 13.5171 8.9009 -0.6962 8.0682 -2.913 41.2742 -0.4894 1.2264 -0.2865 -1.2699 0.5029 -0.2962 -0.565 0.9074 -0.0134 0.7225 0.0019 -0.0025 0.3081 0.0492 0.136 15.0072 -1.3949 -3.8896 46 1.1922 -0.0979 0.5355 2.005 -2.3199 6.3752 -0.0488 0.0081 -0.0351 0.0077 0.0311 -0.0813 -0.0433 -0.0136 0.0177 0.0144 0.0059 0.0051 0.0917 -0.0133 0.1299 18.0354 -11.4066 16.0164 47 2.1507 -0.6457 2.6707 2.6604 -3.6105 10.7839 0.0134 -0.1249 -0.1004 0.1092 -0.0902 -0.0768 -0.0786 0.1554 0.0769 0.0077 0.0034 0.0063 0.1164 -0.0107 0.151 22.9983 -14.9081 21.2437 48 13.5519 -5.6936 4.9195 3.3485 -1.5962 11.7374 0.3535 0.9364 -0.4791 -0.6684 0.0135 0.4611 -0.4013 0.0935 -0.367 0.3384 -0.1599 -0.0997 0.2863 0.0897 0.2059 9.8695 -8.4443 -2.9266
Refinement TLS group Show large table (5 x 48) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A214 - 222 2 X-RAY DIFFRACTION 2 A223 - 236 3 X-RAY DIFFRACTION 3 A237 - 248 4 X-RAY DIFFRACTION 4 A49 - 54 5 X-RAY DIFFRACTION 5 A55 - 83 6 X-RAY DIFFRACTION 6 A84 - 88 7 X-RAY DIFFRACTION 7 A89 - 96 8 X-RAY DIFFRACTION 8 A97 - 103 9 X-RAY DIFFRACTION 9 A104 - 115 10 X-RAY DIFFRACTION 10 A116 - 120 11 X-RAY DIFFRACTION 11 A121 - 128 12 X-RAY DIFFRACTION 12 A129 - 133 13 X-RAY DIFFRACTION 13 B213 - 235 14 X-RAY DIFFRACTION 14 B236 - 242 15 X-RAY DIFFRACTION 15 B243 - 248 16 X-RAY DIFFRACTION 16 B49 - 54 17 X-RAY DIFFRACTION 17 B55 - 79 18 X-RAY DIFFRACTION 18 B80 - 84 19 X-RAY DIFFRACTION 19 B85 - 100 20 X-RAY DIFFRACTION 20 B101 - 105 21 X-RAY DIFFRACTION 21 B106 - 115 22 X-RAY DIFFRACTION 22 B116 - 120 23 X-RAY DIFFRACTION 23 B121 - 135 24 X-RAY DIFFRACTION 24 B136 - 143 25 X-RAY DIFFRACTION 25 C213 - 221 26 X-RAY DIFFRACTION 26 C222 - 227 27 X-RAY DIFFRACTION 27 C228 - 236 28 X-RAY DIFFRACTION 28 C237 - 248 29 X-RAY DIFFRACTION 29 C50 - 79 30 X-RAY DIFFRACTION 30 C80 - 84 31 X-RAY DIFFRACTION 31 C85 - 99 32 X-RAY DIFFRACTION 32 C100 - 104 33 X-RAY DIFFRACTION 33 C105 - 115 34 X-RAY DIFFRACTION 34 C116 - 120 35 X-RAY DIFFRACTION 35 C121 - 129 36 X-RAY DIFFRACTION 36 C130 - 143 37 X-RAY DIFFRACTION 37 D213 - 222 38 X-RAY DIFFRACTION 38 D223 - 233 39 X-RAY DIFFRACTION 39 D234 - 240 40 X-RAY DIFFRACTION 40 D241 - 248 41 X-RAY DIFFRACTION 41 D49 - 54 42 X-RAY DIFFRACTION 42 D55 - 79 43 X-RAY DIFFRACTION 43 D80 - 84 44 X-RAY DIFFRACTION 44 D85 - 96 45 X-RAY DIFFRACTION 45 D97 - 103 46 X-RAY DIFFRACTION 46 D104 - 115 47 X-RAY DIFFRACTION 47 D116 - 129 48 X-RAY DIFFRACTION 48 D130 - 134