Software Name Version Classification HKL-3000data reduction SCALEPACKdata scaling SHELXphasing MLPHAREphasing DM6.3 phasing PHENIXrefinement PDB_EXTRACT3.15 data extraction
Refinement Method to determine structure : SAD / Resolution : 2→28.672 Å / SU ML : 0.18 / Cross valid method : FREE R-VALUE / σ(F) : 1.93 / Phase error : 19.03 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.1916 2079 4.87 % Random Selection Rwork 0.1526 40580 - - obs 0.1545 25528 89.03 % -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 127.79 Å2 / Biso mean : 36.0733 Å2 / Biso min : 12.72 Å2 Refinement step Cycle : final / Resolution : 2→28.672 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 2437 0 230 241 2908 Biso mean - - 34.29 39.02 - Num. residues - - - - 332
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.01 2671 X-RAY DIFFRACTION f_angle_d1.528 3693 X-RAY DIFFRACTION f_chiral_restr0.046 392 X-RAY DIFFRACTION f_plane_restr0.007 463 X-RAY DIFFRACTION f_dihedral_angle_d13.455 889
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Rms Type 1 1 A1814 X-RAY DIFFRACTION 20.341 TORSIONAL1 2 B1814 X-RAY DIFFRACTION 20.341 TORSIONAL1 3 C1814 X-RAY DIFFRACTION 20.341 TORSIONAL
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 15
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.9989-2.0454 0.2279 61 0.2281 1045 1106 34 2.0454-2.0965 0.2071 67 0.1962 1533 1600 51 2.0965-2.1532 0.2392 102 0.1767 2094 2196 69 2.1532-2.2165 0.2261 117 0.1793 2700 2817 87 2.2165-2.2881 0.1697 165 0.1665 2886 3051 96 2.2881-2.3698 0.2365 138 0.1628 3046 3184 100 2.3698-2.4646 0.2113 162 0.159 2992 3154 100 2.4646-2.5767 0.2122 149 0.1639 3072 3221 100 2.5767-2.7125 0.1955 152 0.1623 3038 3190 100 2.7125-2.8823 0.2075 170 0.1605 3022 3192 100 2.8823-3.1046 0.2195 136 0.1613 3065 3201 100 3.1046-3.4166 0.2016 170 0.1644 3013 3183 100 3.4166-3.9099 0.1902 185 0.1425 2994 3179 100 3.9099-4.922 0.1708 150 0.1191 3037 3187 100 4.922-28.6751 0.1471 155 0.1401 3043 3198 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 18) 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 3.2182 3.9964 -1.1562 5.0557 -2.0059 3.8493 -0.197 0.1176 0.2759 0.2405 0.1052 0.8455 -0.3578 -1.1266 0.0975 0.2523 0.0427 -0.0162 0.4453 -0.1396 0.2901 35.8032 -6.4909 -1.6079 2 4.2161 -2.6828 -0.2256 6.9324 -0.0392 1.7517 -0.0698 -0.0578 -0.2347 0.0212 -0.0076 0.0693 0.1733 -0.1688 0.0841 0.165 -0.0268 -0.0027 0.1993 -0.036 0.1128 45.7342 -11.6141 2.9466 3 5.6635 -2.7958 -3.7098 2.0562 0.4215 7.5649 -0.2452 -0.9684 -0.184 0.2589 0.2486 -0.1653 0.2287 0.4833 0.0557 0.154 0.0143 -0.0118 0.2296 -0.044 0.2175 54.8765 -8.9595 8.8987 4 2.41 1.0235 2.7164 2.7838 -0.7596 4.6273 -0.0772 0.0911 0.2911 -0.1384 -0.1264 -0.1044 -0.314 -0.0617 0.2023 0.1691 -0.0064 0.0009 0.1167 0.0071 0.1521 51.365 -1.6282 0.0102 5 7.9941 -0.0758 -4.2355 6.5094 0.8943 2.4082 -0.1195 -0.7719 0.4137 -0.1537 0.4891 -0.8974 -0.2312 1.1198 -0.3722 0.1891 -0.0569 -0.0198 0.339 -0.0336 0.2979 61.6271 -1.5926 8.0879 6 3.0472 -2.3786 -0.5269 4.6774 -1.815 1.8439 0.0284 0.348 0.8784 0.0322 -0.3398 -0.6123 -0.396 0.3197 0.3782 0.2664 -0.0124 -0.0267 0.2186 0.0656 0.3152 47.375 10.8087 14.4654 7 6.3409 0.1664 1.7109 4.6184 0.0341 2.8406 -0.0038 0.4493 0.779 -0.0515 -0.2937 0.2362 -0.4982 -0.3052 0.227 0.3493 0.0937 0.0014 0.231 -0.0125 0.3209 36.2813 15.0704 13.5101 8 5.097 -2.2324 0.1831 2.6662 -0.6676 4.3726 -0.0341 -0.3768 0.2401 0.0374 -0.1482 0.8 -0.3227 -0.5876 0.3107 0.3513 0.0347 0.0239 0.3053 -0.2081 0.5201 25.7617 13.2946 16.6163 9 4.766 0.0692 1.8785 2.543 -0.0569 2.2493 0.5033 0.0818 -0.4534 -0.0774 -0.4989 0.8679 0.3128 -0.3741 -0.0019 0.3158 0.0205 -0.0428 0.27 -0.1561 0.4057 28.8347 4.2716 14.3881 10 6.2615 5.605 -5.1632 5.0673 -4.5554 4.9313 0.006 -0.0798 -0.3524 -0.1286 -0.0069 -1.3445 0.7234 0.4102 0.0135 0.3631 0.1416 -0.0325 0.4398 -0.1411 0.4691 35.2027 6.1295 35.9924 11 7.3025 -5.0516 -0.3216 5.864 -2.0361 2.171 0.1287 -0.0405 -0.6392 -0.1736 0.0321 0.7463 -0.0097 -0.0358 -0.1302 0.221 -0.02 -0.0032 0.1822 -0.012 0.2882 39.4004 -4.4132 27.9601 12 7.9979 -4.7096 -5.5365 7.115 3.3397 3.9832 0.0851 0.86 -0.6535 -0.6043 -0.33 0.4508 0.5627 0.0215 0.2905 0.2663 0.0588 -0.0271 0.34 -0.0371 0.2401 48.6151 -8.8287 21.0813 13 1.5855 2.7626 -1.4414 7.1083 0.343 4.8636 0.01 1.0582 -1.2109 -0.8463 -0.2189 -0.7016 0.8322 0.6591 0.1732 0.3284 0.1957 -0.026 0.4807 -0.0987 0.3975 54.1554 -14.3095 24.4054 14 5.659 1.1254 2.8451 8.093 -0.9731 4.4417 -0.0887 -0.7645 -0.7543 0.6374 0.1738 0.0525 -0.17 -0.2921 -0.0569 0.2913 0.0027 0.0712 0.2489 0.0628 0.227 43.8556 -7.1726 34.9826 15 7.3741 -1.7766 -0.3632 7.6547 2.5242 0.8425 -0.0954 0.0028 -0.5765 0.4389 -0.2563 -0.5997 0.7498 0.8975 0.1718 0.3007 0.106 -0.0421 0.4598 0.1323 0.304 57.6089 -10.4768 32.3918 16 4.515 -3.1465 -1.4951 5.4549 1.1905 2.3157 0.0955 0.1561 0.1744 -0.1349 -0.4867 -0.6969 -0.0787 0.9058 0.1896 0.2297 0.006 0.0146 0.4395 0.1504 0.273 55.6847 -2.2293 24.0135 17 6.434 -0.4905 1.2757 2.5396 2.2029 3.6673 -0.169 -0.6563 0.5761 0.7151 -0.094 -0.4826 -0.4148 0.3684 0.2401 0.4162 -0.1128 -0.1259 0.2797 0.0154 0.2408 52.5276 3.3488 33.0276 18 3.9835 -1.1364 1.7085 0.7886 -0.0561 1.4032 -0.0287 0.0546 0.1367 0.0042 -0.0502 -0.1406 -0.0509 0.1538 -0 0.3215 -0.0979 -0.2823 0.7051 0.3381 0.7348 64.8392 -4.5556 32.8113
Refinement TLS group Show large table (6 x 18) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 34 through 51 )A0 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 52 through 87 )A0 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 88 through 103 )A0 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 104 through 131 )A0 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 132 through 144 )A0 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 34 through 51 )B0 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 52 through 87 )B0 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 88 through 103 )B0 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 104 through 144 )B0 10 X-RAY DIFFRACTION 10 chain 'C' and (resid 34 through 38 )C0 11 X-RAY DIFFRACTION 11 chain 'C' and (resid 39 through 51 )C0 12 X-RAY DIFFRACTION 12 chain 'C' and (resid 52 through 60 )C0 13 X-RAY DIFFRACTION 13 chain 'C' and (resid 61 through 67 )C