Software Name Version Classification CrystalCleardata collection PHASERphasing PHENIX(phenix.refine: 1.5_2)refinement HKL-2000data reduction HKL-2000data scaling
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : Teg12 ternary, pdb code 3MGBResolution : 2.7→22.786 Å / SU ML : 0.33 / Isotropic thermal model : isotropic / Cross valid method : THROUGHOUT / σ(F) : 0.08 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.2356 678 4.97 % Random Rwork 0.1955 - - - obs 0.1975 13643 89.76 % - all - 14585 - -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 79.853 Å2 / ksol : 0.365 e/Å3 Displacement parameters Baniso -1 Baniso -2 Baniso -3 1- 4.4918 Å2 0 Å2 -0 Å2 2- - 4.4918 Å2 0 Å2 3- - - -8.9835 Å2
Refinement step Cycle : LAST / Resolution : 2.7→22.786 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 1797 0 25 54 1876
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.004 1859 X-RAY DIFFRACTION f_angle_d0.805 2521 X-RAY DIFFRACTION f_dihedral_angle_d14.59 654 X-RAY DIFFRACTION f_chiral_restr0.052 285 X-RAY DIFFRACTION f_plane_restr0.004 321
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.7004-2.9085 0.3508 123 0.282 2222 X-RAY DIFFRACTION 79 2.9085-3.2005 0.303 117 0.2227 2326 X-RAY DIFFRACTION 81 3.2005-3.6619 0.2103 149 0.1809 2661 X-RAY DIFFRACTION 93 3.6619-4.6074 0.2142 150 0.1582 2825 X-RAY DIFFRACTION 98 4.6074-22.7867 0.213 139 0.1976 2931 X-RAY DIFFRACTION 97
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 15) 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 1.1224 -0.0979 0.4967 0.4728 -0.7904 1.3974 -0.1365 0.1187 0.465 0.0879 0.1037 0.0129 -0.0019 -0.1867 -0.0001 0.2732 -0.0728 0.0064 0.279 -0.0004 0.3194 38.6554 -31.0358 -25.7622 2 0.4298 0.1307 0.4815 0.2447 0.1186 0.6956 0.0723 0.7348 -0.4821 -0.0243 0.4518 -0.4553 -0.1068 0.9596 0.022 0.5049 -0.0543 -0.0059 0.3202 0.0022 0.3311 54.4154 -35.3535 -28.4113 3 0.2651 0.0725 0.3132 0.4315 -0.2051 0.5573 -0.1055 0.4843 1.1102 0.1199 -0.075 -0.3486 -0.654 -0.0688 0.0006 0.3457 -0.0483 -0.0113 0.2566 0.0483 0.3288 48.6383 -26.1737 -21.4024 4 0.2604 0.0355 0.1606 0.4247 -0.4786 0.677 -0.1612 -0.1816 0.3465 0.1178 -0.1461 0.8226 -0.1719 0.1568 0.0006 0.2318 -0.0651 -0.0235 0.3755 0.001 0.3244 52.8211 -30.5503 -13.5689 5 2.8571 -1.1508 1.0174 0.6404 -0.5056 0.417 0.7925 0.4486 -2.5544 0.7609 0.7005 2.0169 1.7553 -0.5942 0.0368 0.6947 -0.1584 -0.0426 0.4505 0.0114 0.7509 50.6857 -47.9858 -15.4404 6 0.1181 0.144 -0.152 0.1659 -0.1793 0.1896 -0.1651 -0.7365 -0.8098 0.6666 0.5417 0.7587 -0.1613 -1.0264 -0.0021 0.5111 -0.0362 0.0467 0.5812 0.1726 0.4826 40.4987 -40.7667 -12.6568 7 0.4145 0.3252 0.1124 0.2551 0.1244 0.3192 -0.2305 -0.3866 0.3903 -0.6093 0.4909 -0.4726 0.1523 0.5242 0.001 0.2774 -0.1737 0.0403 0.459 -0.035 0.4135 27.2437 -39.5568 -20.4042 8 0.0444 -0.0391 -0.0256 0.1561 -0.0874 0.0917 -0.2469 1.15 0.5555 -0.0979 -0.3428 0.1465 0.0406 -0.8382 -0.0006 0.2553 -0.1059 -0.0456 0.5557 -0.0057 0.4074 27.3987 -31.9227 -29.7818 9 0.4631 -0.0505 -0.0271 0.0149 -0.0061 0.0114 -0.9747 -0.8676 -0.8394 1.0062 -0.4247 -2.0863 0.1232 0.4133 0.0001 0.7309 -0.0729 0.2091 0.3472 0.1928 0.6312 48.6268 -48.1953 -34.3775 10 4.3579 -2.8105 -1.7513 3.0015 1.324 1.7938 -0.8204 0.2215 -1.4153 -0.1649 0.5171 0.4698 1.8901 -0.2892 -0.0737 0.9107 -0.1995 0.2379 0.2738 -0.233 0.7684 42.5001 -53.9483 -39.9293 11 1.2294 -0.0208 -0.2866 1.0716 0.4765 1.1216 0.1124 0.9264 0.0359 -0.8635 -0.2962 0.0932 -0.3287 -1.2354 -0.0134 0.388 -0.0674 -0.0928 0.5309 0.0458 0.3526 35.5298 -33.684 -36.7007 12 0.0769 0.0364 -0.0406 0.0402 -0.0317 0.0273 0.6104 -0.3628 -0.145 -0.4927 -0.1828 0.0347 0.3954 0.9898 0.0043 0.9493 0.0556 0.2763 0.4237 -0.1377 0.8996 54.5776 -55.0434 -40.2967 13 0.3738 0.2075 -0.2651 0.1305 -0.1309 0.1902 -0.3732 0.7675 -0.0482 -0.5748 -0.0817 0.1043 0.043 -1.0929 -0.0001 0.6285 -0.2308 0.2821 0.4706 -0.1713 0.4844 50.353 -48.1628 -47.2467 14 0.554 0.1064 -0.3192 0.263 -0.137 0.2033 -0.7898 1.2986 0.3419 0.1948 0.3281 0.4569 0.2231 -1.136 -0.0003 0.4923 -0.1942 0.0132 0.4803 -0.0727 0.3015 47.2975 -36.4494 -43.7925 15 0.7499 0.4922 0.2602 1.2437 0.7471 1.8386 0.2166 -0.4624 -0.2425 0.6823 -0.0992 0.2721 0.7963 -0.2223 0.0028 0.1596 0.0184 -0.012 0.2906 0.0124 0.277 45.9061 -35.9029 -16.4765
Refinement TLS group ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain A and (resid 0:12) or chain A and (resid 57:67) or chain A and (resid 83:90) or chain A and (resid 157:165)2 X-RAY DIFFRACTION 2 chain A and (resid 166:170)3 X-RAY DIFFRACTION 3 chain A and (resid 171:186)4 X-RAY DIFFRACTION 4 chain A and (resid 187:203)5 X-RAY DIFFRACTION 5 chain A and (resid 204:211)6 X-RAY DIFFRACTION 6 chain A and (resid 31:42)7 X-RAY DIFFRACTION 7 chain A and (resid 43:56)8 X-RAY DIFFRACTION 8 chain A and (resid 68:82)9 X-RAY DIFFRACTION 9 chain A and (resid 91:101)10 X-RAY DIFFRACTION 10 chain A and (resid 109:127)11 X-RAY DIFFRACTION 11 chain A and (resid 133:156)12 X-RAY DIFFRACTION 12 chain A and (resid 241:248)13 X-RAY DIFFRACTION 13 chain A and (resid 249:261)14 X-RAY DIFFRACTION 14 chain A and (resid 262:275)15 X-RAY DIFFRACTION 15 chain A and (resid