Software Name Version Classification HKL-3000data collection MOLREPphasing REFMAC5.5.0110refinement HKL-3000data reduction HKL-3000data scaling
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB entry 1vicResolution : 1.75→25.06 Å / Cor.coef. Fo :Fc : 0.964 / Cor.coef. Fo :Fc free : 0.95 / SU B : 7.131 / SU ML : 0.1 / Isotropic thermal model : Isotropic / Cross valid method : THROUGHOUT / ESU R : 0.133 / ESU R Free : 0.125 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.23209 4919 5 % RANDOM Rwork 0.19806 - - - obs 0.19979 93730 100 % - all - 93730 - -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.4 Å / Solvent model : MASKDisplacement parameters Biso mean : 37.235 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.42 Å2 -1.05 Å2 0.56 Å2 2- - 0.36 Å2 -1.6 Å2 3- - - 0.63 Å2
Refinement step Cycle : LAST / Resolution : 1.75→25.06 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 7768 0 1 690 8459
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_d0.009 0.022 7979 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.228 1.957 10898 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg9.818 5 1014 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.874 24.429 359 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.86 15 1295 X-RAY DIFFRACTION r_dihedral_angle_4_deg15.395 15 56 X-RAY DIFFRACTION r_chiral_restr0.086 0.2 1247 X-RAY DIFFRACTION r_gen_planes_refined0.01 0.021 6124 X-RAY DIFFRACTION r_gen_planes_otherX-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_it0.475 1.5 5062 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it0.882 2 8214 X-RAY DIFFRACTION r_scbond_it1.557 3 2917 X-RAY DIFFRACTION r_scangle_it2.654 4.5 2680 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
LS refinement shell Resolution : 1.753→1.798 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.322 351 - Rwork 0.287 6714 - obs - - 100 %
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 5.1089 1.9337 -0.043 9.5482 1.2706 4.4677 -0.1261 0.2946 -0.2186 -0.0825 -0.0079 0.134 0.2031 0.0491 0.1341 0.1719 0.0031 0.0216 0.151 -0.03 0.1316 46.9608 28.2512 -14.379 2 3.0333 2.0117 0.9965 5.79 2.578 7.092 -0.1683 0.0456 0.3872 -0.2178 -0.2261 0.4908 -0.2473 -0.7298 0.3944 0.1788 0.0017 -0.0193 0.0941 -0.0152 0.2337 56.0423 46.4821 -5.2978 3 3.205 1.1063 0.1559 2.3473 0.2857 1.7796 -0.1351 0.4312 0.0491 -0.2632 0.0487 -0.0896 -0.0974 0.1349 0.0865 0.1802 -0.0096 0.0398 0.1711 0.0117 0.0739 56.8775 34.9803 -15.7941 4 7.6757 3.1434 -0.4464 3.8924 -1.1178 3.437 0.9764 -0.358 1.1306 0.4331 -1.0043 0.9192 -0.6458 -0.0468 0.0279 0.2596 -0.028 0.0811 0.411 -0.2024 0.2834 41.7308 42.3289 -14.3861 5 2.3453 -0.4285 0.1059 1.7537 -0.1254 1.6513 -0.0325 0.2586 -0.1178 -0.2375 -0.0013 0.126 -0.1237 -0.1075 0.0338 0.1732 0.0077 0.0013 0.1359 -0.0161 0.1484 46.9389 28.3346 -11.6186 6 2.081 0.7062 0.7023 2.2036 1.1753 4.2591 -0.0372 -0.2158 -0.2003 0.0544 0.1267 -0.0917 0.0289 0.1656 -0.0895 0.1137 0.0346 0.0066 0.1554 0.0163 0.1933 42.685 23.4798 1.8328 7 1.9196 0.1293 -0.698 1.3302 -0.0587 1.855 0.0507 -0.2853 -0.0356 0.1336 -0.0683 -0.0357 -0.0024 0.1471 0.0176 0.1301 0.0068 -0.0036 0.1711 0.0203 0.1569 37.7502 27.8114 12.0824 8 1.8492 0.1286 -0.4314 0.7748 -0.0792 0.9628 0.0585 -0.0615 0.0179 0.0231 -0.0039 -0.0169 -0.2206 0.0696 -0.0546 0.1859 0.0262 -0.0033 0.1267 -0.0075 0.1744 37.5027 30.8218 3.3396 9 2.1259 -0.5218 -0.6157 1.3241 0.6043 0.8032 0.0374 0.0502 0.0179 -0.0358 -0.02 0.0527 -0.1166 -0.0704 -0.0174 0.158 0.0235 -0.0008 0.1263 0.0303 0.1661 34.7605 31.4115 0.6211 10 2.4528 0.4228 0.3015 2.5282 -0.178 0.2776 0.1029 -0.1203 -0.0038 0.012 -0.0712 -0.0796 0.0118 0.102 -0.0317 0.1992 -0.0047 -0.0102 0.1262 -0.0035 0.1252 64.3963 33.2682 -0.4712 11 5.5458 0.21 -0.1303 4.6496 1.855 3.3159 0.1805 0.0146 -0.1912 0.5142 -0.0138 -0.0945 0.5057 0.2053 -0.1667 0.1615 -0.0463 -0.0206 0.2283 -0.0335 0.1179 9.3671 18.7454 25.9644 12 1.897 -0.1137 0.6624 4.436 0.6526 7.3463 0.1269 -0.1115 -0.0291 0.5521 -0.021 0.1976 0.1999 -0.239 -0.1059 0.1024 -0.0624 0.0538 0.2255 -0.0129 0.0852 5.6767 22.8204 31.3534 13 3.0996 -3.8486 -3.0767 7.4089 0.102 8.9786 -0.2641 -0.2095 -0.3656 0.5056 -0.2316 0.1548 0.5126 0.7147 0.4958 0.3895 -0.1732 -0.1944 0.2685 0.1193 0.2315 9.4051 12.4752 31.3523 14 2.1558 0.6001 -0.7878 3.1804 1.228 1.3421 -0.0078 0.122 -0.2117 0.1425 0.0637 -0.0062 0.0717 -0.1616 -0.0559 0.086 -0.0201 0.0022 0.2506 -0.0311 0.1213 8.0754 19.4671 19.8193 15 2.4271 1.0351 0.4912 2.2907 0.4284 1.6558 0.0808 -0.3035 0.0421 -0.0542 -0.102 0.0094 -0.1036 -0.16 0.0212 0.113 0.0319 0.0282 0.219 -0.0168 0.1395 16.1064 31.4003 13.6894 16 1.9437 0.6382 -0.1523 1.379 0.1222 1.6817 0.1158 -0.2264 0.1825 0.1364 -0.0771 -0.0028 -0.1401 -0.0252 -0.0387 0.1438 0.0205 0.0146 0.1592 -0.0141 0.1456 28.3294 36.407 15.4221 17 16.8594 -11.9312 -3.2754 9.824 4.7597 5.0191 0.1821 0.2963 -0.1837 -0.0478 -0.5045 0.2206 0.1036 -0.4573 0.3224 0.0806 -0.0803 0.0273 0.2571 0.1675 0.3461 16.9989 13.9271 12.9187 18 2.2852 -0.1112 -0.2252 1.4839 0.4006 1.4346 0.0135 -0.142 -0.3285 0.039 -0.0508 0.0358 0.1035 -0.0284 0.0373 0.1487 -0.0052 0.0294 0.1551 0.0488 0.1579 24.8798 21.4483 13.4369 19 1.9168 0.5301 -4.2491 7.2191 -3.0259 11.7853 0.2195 0.1057 0.1336 0.6562 -0.1312 -0.6784 -0.3829 0.5717 -0.0884 0.2924 -0.0342 -0.0218 0.385 0.0107 0.0849 13.6995 33.6947 34.3916 20 5.9939 0.2273 -4.1468 44.0302 -36.7981 39.7639 0.4035 0.1496 1.5882 0.41 -0.197 -0.7701 -1.2612 -1.1285 -0.2064 0.5902 0.0654 0.1921 0.2954 -0.0339 0.4785 3.7567 38.8932 36.5894 21 7.8088 4.4391 1.4129 8.6825 3.4852 3.8809 -0.0671 0.0478 0.1942 -0.1819 0.1278 0.3659 -0.1513 0.0207 -0.0607 0.1903 -0.033 0.002 0.1813 -0.0076 0.1156 -21.5537 -3.8115 19.2785 22 4.2634 0.8204 -0.5626 4.7481 0.276 1.03 -0.0608 -0.2504 -0.1607 0.3751 0.0807 0.4016 0.0668 0.0222 -0.0198 0.1603 -0.044 0.0594 0.1645 0.0225 0.0842 -23.7233 -11.1537 22.4743 23 6.3302 0.276 -1.7011 9.3449 -2.6937 2.5794 -0.0674 -0.0967 0.1995 0.2251 0.2967 1.0631 -0.0982 -0.3415 -0.2293 0.0961 -0.0297 0.101 0.1763 -0.0348 0.2504 -31.7697 -2.9356 21.6535 24 9.7917 -2.1709 0.5126 9.0887 0.8227 5.699 -0.285 -0.137 0.2341 0.2178 0.4338 0.1176 -0.2561 0.0679 -0.1487 0.1117 -0.001 0.0132 0.0499 -0.0584 0.222 -20.8272 6.6723 18.3222 25 3.8792 2.0457 -0.678 3.4968 -0.0345 0.8565 0.0456 -0.3059 0.0244 0.1341 -0.0347 -0.051 0.0254 0.0648 -0.0109 0.1543 -0.039 -0.0296 0.1776 -0.0218 0.1052 -9.9638 -4.5653 19.8077 26 0.9097 0.4449 -0.5205 1.4109 0.4485 1.7857 -0.004 -0.0593 -0.1043 0.0039 -0.0337 -0.0491 0.1918 0.1242 0.0377 0.1433 0.0253 -0.0258 0.0976 0.0214 0.1816 -3.2282 -8.9727 2.9439 27 3.6416 -1.0962 -3.3169 2.3466 2.4625 6.7029 0.0588 0.1178 -0.3817 -0.0958 -0.1097 -0.1554 0.2913 0.1344 0.0509 0.1568 0.0715 -0.0287 0.0561 0.0102 0.193 0.491 -15.3345 -0.7772 28 0.6796 0.3335 0.7672 7.1182 -6.6785 8.0526 0.0245 -0.1816 0.1199 0.0956 -0.2856 -0.0501 -0.0437 -0.0937 0.2611 0.0515 0.024 -0.0063 0.2346 -0.1584 0.2803 -13.3007 8.4661 11.9374 29 1.213 0.5531 0.294 1.6996 -0.1061 2.0083 0.0096 -0.0956 0.1041 0.007 -0.0753 0.1269 -0.0647 -0.1415 0.0657 0.1134 0.0277 -0.0071 0.1093 -0.0096 0.2004 -8.6434 0.6995 5.4372 30 6.6808 -0.3249 2.5682 4.6494 -1.5908 9.0852 -0.0329 -0.017 -0.708 0.1574 0.0036 -0.2276 0.3004 0.2093 0.0293 0.1336 -0.04 0.0312 0.0823 -0.0295 0.2571 -21.7385 -23.5395 17.0239 31 5.2292 0.5782 -0.1144 0.5566 -0.2079 7.4247 -0.0045 0.2459 0.2441 -0.0004 0.1552 0.178 -0.2237 -0.1359 -0.1508 0.1981 -0.1147 0.0673 0.1396 -0.0104 0.1394 20.7054 14.4134 -13.3423 32 15.7025 -5.7346 -0.1102 22.4697 -6.9787 15.4898 0.1535 1.1104 -2.2234 1.0024 0.3757 -1.8594 0.98 0.8722 -0.5292 0.3533 0.0615 -0.2564 0.2864 -0.4276 0.8474 23.834 -3.0234 -25.3375 33 6.0166 -1.7936 -0.9666 4.3401 1.6315 4.4871 -0.078 0.7758 0.1489 -0.13 0.091 -0.3562 -0.1616 0.5014 -0.013 0.1642 -0.1295 0.0694 0.2553 -0.019 0.0713 23.5188 11.0441 -21.8904 34 15.7151 -3.0692 0.3004 0.8662 2.0181 17.6669 -0.667 0.1864 -1.1708 0.3364 0.1398 0.1982 1.6848 1.0879 0.5272 0.3015 0.0091 0.1722 0.2042 -0.2011 0.5589 30.3808 3.5062 -16.3526 35 4.1709 0.9932 2.7376 1.0991 1.3356 3.5757 0.0641 0.1369 -0.0982 -0.0145 0.0764 -0.2234 0.2585 0.0463 -0.1405 0.2066 -0.073 0.0541 0.1329 0.0028 0.089 20.1367 11.2279 -12.8234 36 2.0223 0.6702 -0.1039 1.4787 -0.5771 0.5863 -0.1085 0.2192 -0.0531 -0.2353 0.1652 0.0492 -0.0581 0.0438 -0.0567 0.2283 -0.0139 -0.011 0.1381 -0.0078 0.1408 1.5911 4.0042 -9.317 37 4.4076 2.334 0.8807 2.2561 0.5795 1.4406 -0.0659 0.1554 -0.1812 -0.2524 0.1103 -0.0143 -0.0107 0.0043 -0.0444 0.2065 -0.0015 -0.0329 0.1087 0.0037 0.138 0.2692 1.566 -10.3849 38 9.4668 10.9889 3.1459 13.6197 5.8323 6.5648 0.2459 -0.6933 -0.6637 0.4433 -0.1106 -0.7042 0.4319 1.5831 -0.1353 0.0314 0.0943 -0.0371 0.6472 0.0724 0.2956 14.332 -3.5557 1.1017 39 1.7477 0.0983 -0.0519 3.1168 -2.1382 4.7527 0.015 -0.0803 -0.125 -0.018 0.0516 -0.1578 -0.3693 0.3525 -0.0666 0.1179 -0.0503 0.0156 0.1521 -0.0353 0.1355 8.1963 5.1489 -3.6454 40 7.15 -2.9074 -0.4006 2.5972 1.8053 11.0922 0.2848 0.9816 -0.6232 0.0297 -0.2583 0.3114 0.1777 -0.0723 -0.0266 0.2279 -0.1012 0.0564 0.298 -0.1545 0.1003 12.397 1.8856 -31.2007
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 - 9 2 X-RAY DIFFRACTION 2 A10 - 19 3 X-RAY DIFFRACTION 3 A20 - 65 4 X-RAY DIFFRACTION 4 A66 - 83 5 X-RAY DIFFRACTION 5 A84 - 111 6 X-RAY DIFFRACTION 6 A112 - 134 7 X-RAY DIFFRACTION 7 A135 - 166 8 X-RAY DIFFRACTION 8 A167 - 203 9 X-RAY DIFFRACTION 9 A204 - 228 10 X-RAY DIFFRACTION 10 A229 - 252 11 X-RAY DIFFRACTION 11 B1 - 13 12 X-RAY DIFFRACTION 12 B14 - 51 13 X-RAY DIFFRACTION 13 B52 - 78 14 X-RAY DIFFRACTION 14 B79 - 110 15 X-RAY DIFFRACTION 15 B111 - 134 16 X-RAY DIFFRACTION 16 B135 - 184 17 X-RAY DIFFRACTION 17 B185 - 198 18 X-RAY DIFFRACTION 18 B199 - 228 19 X-RAY DIFFRACTION 19 B229 - 243 20 X-RAY DIFFRACTION 20 B244 - 251 21 X-RAY DIFFRACTION 21 C1 - 13 22 X-RAY DIFFRACTION 22 C14 - 49 23 X-RAY DIFFRACTION 23 C50 - 72 24 X-RAY DIFFRACTION 24 C73 - 92 25 X-RAY DIFFRACTION 25 C93 - 123 26 X-RAY DIFFRACTION 26 C124 - 163 27 X-RAY DIFFRACTION 27 C164 - 184 28 X-RAY DIFFRACTION 28 C185 - 199 29 X-RAY DIFFRACTION 29 C200 - 231 30 X-RAY DIFFRACTION 30 C232 - 251 31 X-RAY DIFFRACTION 31 D1 - 8 32 X-RAY DIFFRACTION 32 D9 - 26 33 X-RAY DIFFRACTION 33 D27 - 51 34 X-RAY DIFFRACTION 34 D52 - 79 35 X-RAY DIFFRACTION 35 D80 - 110 36 X-RAY DIFFRACTION 36 D111 - 163 37 X-RAY DIFFRACTION 37 D164 - 193 38 X-RAY DIFFRACTION 38 D194 - 208 39 X-RAY DIFFRACTION 39 D209 - 228 40 X-RAY DIFFRACTION 40 D229 - 250