Software Name Version Classification DNAdata collection MOLREPphasing PHENIX(phenix.refine: 1.7.3_928)refinement XDSdata reduction SCALAdata scaling
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB entry 4IP2Resolution : 2.3→49.212 Å / Isotropic thermal model : Anisotropic / σ(F) : 4.1 / σ(I) : 4.1 / Phase error : 26.99 / Stereochemistry target values : TWIN_LSQ_FRfactor Num. reflection % reflection Selection details Rfree 0.2191 5145 5.09 % RANDOM Rwork 0.1643 - - - obs 0.1668 101106 98.66 % - all - 102479 - -
Solvent computation Shrinkage radii : 0.73 Å / VDW probe radii : 1 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 14.346 Å2 / ksol : 0.346 e/Å3 Displacement parameters Biso mean : 26.4 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.3838 Å2 -0 Å2 2.2037 Å2 2- - -3.9518 Å2 -0 Å2 3- - - 4.3356 Å2
Refinement step Cycle : LAST / Resolution : 2.3→49.212 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 15317 0 5 247 15569
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 15745 X-RAY DIFFRACTION f_angle_d1.1 21498 X-RAY DIFFRACTION f_dihedral_angle_d14.049 5700 X-RAY DIFFRACTION f_chiral_restr0.073 2330 X-RAY DIFFRACTION f_plane_restr0.006 2858
LS refinement shell Show large table (7 x 20) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.3-2.3398 0.2849 263 0.2018 4784 X-RAY DIFFRACTION 94 2.3398-2.3824 0.2864 259 0.1991 4755 X-RAY DIFFRACTION 94 2.3824-2.4282 0.3093 260 0.1996 4894 X-RAY DIFFRACTION 95 2.4282-2.4777 0.2721 237 0.1987 4731 X-RAY DIFFRACTION 95 2.4777-2.5316 0.2691 295 0.1942 4818 X-RAY DIFFRACTION 94 2.5316-2.5905 0.2882 240 0.1928 4771 X-RAY DIFFRACTION 95 2.5905-2.6553 0.2538 264 0.1851 4826 X-RAY DIFFRACTION 94 2.6553-2.727 0.2412 231 0.1858 4755 X-RAY DIFFRACTION 95 2.727-2.8073 0.2261 266 0.1831 4857 X-RAY DIFFRACTION 94 2.8073-2.8979 0.256 226 0.1796 4814 X-RAY DIFFRACTION 95 2.8979-3.0014 0.2261 233 0.1803 4804 X-RAY DIFFRACTION 95 3.0014-3.1216 0.2375 264 0.1778 4825 X-RAY DIFFRACTION 94 3.1216-3.2636 0.2262 223 0.1722 4810 X-RAY DIFFRACTION 94 3.2636-3.4356 0.225 269 0.1608 4739 X-RAY DIFFRACTION 93 3.4356-3.6507 0.2019 263 0.1555 4805 X-RAY DIFFRACTION 93 3.6507-3.9324 0.1825 246 0.142 4813 X-RAY DIFFRACTION 93 3.9324-4.3278 0.1957 247 0.1364 4803 X-RAY DIFFRACTION 93 4.3278-4.9532 0.1591 250 0.1306 4766 X-RAY DIFFRACTION 92 4.9532-6.2374 0.1991 253 0.1542 4817 X-RAY DIFFRACTION 92 6.2374-42.6627 0.1813 249 0.1447 4850 X-RAY DIFFRACTION 91
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 17) 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 0.7554 0.0171 0.0736 0.6797 0.2449 0.7009 0.0201 -0.0123 -0.0875 0.0206 -0.0268 0.1153 -0.0567 -0.0382 -0.0099 0.0741 0.0204 0.0371 0.0458 0.0169 0.1085 6.3099 -6.7075 75.2494 2 0.3717 -0.1042 -0.0616 0.2676 0.2052 0.3948 0.0264 -0.0814 0.1089 0.0838 -0.0004 0.016 -0.0853 0.0388 -0.0249 0.1668 -0.0137 0.0364 0.0788 0.0042 0.091 17.0758 2.9545 82.7003 3 0.541 -0.1542 0.1886 0.5964 -0.3524 0.4832 0.0131 0.0078 0.1039 -0.1059 -0.0585 -0.175 -0.1223 0.1162 0.0218 0.1985 -0.0187 0.053 0.0923 -0.0148 0.1221 22.9894 9.7521 85.5698 4 0.1451 -0.0504 -0.2357 0.0947 0.1978 0.5548 0.0482 -0.0503 0.0649 0.027 0.0206 -0.0131 -0.0793 0.0949 -0.0476 0.0934 0.0174 0.0216 0.0551 0.0028 0.0859 27.2654 -0.7171 71.6296 5 0.2685 0.0962 0.1033 0.2728 0.1394 0.536 -0.0029 -0.0264 0.0893 0.0239 -0.0552 0.0075 -0.0146 0.0639 0.0108 0.0541 0.0048 0.0218 0.0187 -0.0162 0.0718 30.0646 -4.1559 51.5277 6 0.6629 0.061 0.0439 0.3818 0.1328 0.4392 0.0208 -0.027 -0.04 -0.0217 0.0016 -0.0542 0.1009 -0.0554 -0.0081 0.1036 0.0026 0.0112 0.044 0.0091 0.0527 12.0182 -23.6626 31.3814 7 0.8099 0.3447 -0.0897 0.5579 0.1492 0.2716 0.0725 0.0189 -0.2787 0.1323 -0.0234 -0.2641 0.0409 0.1396 -0.0463 0.1563 0.021 -0.0078 0.1255 0.0028 0.168 25.0314 -31.5246 24.7994 8 0.229 0.0666 0.2566 0.1035 -0.0047 0.3568 0.028 0.043 -0.0694 -0.035 0.0109 -0.0394 0.0861 0.0389 -0.0171 0.0914 0.0268 0.03 0.0325 0.0047 0.0614 28.579 -23.1986 41.4495 9 0.7153 -0.1779 -0.5271 0.1392 0.0164 0.626 -0.1123 0.0188 -0.1167 -0.0086 -0.0073 0.0769 0.1321 -0.0134 0.0222 0.0695 -0.0026 0.033 0.0571 -0.0208 0.1658 24.1612 -21.1173 65.3656 10 0.4146 0.0838 0.0981 0.3887 -0.2142 0.4446 0.0046 0.0746 -0.1012 -0.0018 0.0335 0.0376 0.1484 0.1742 -0.0163 0.0994 0.0479 0.0273 0.1127 -0.0093 0.1129 -14.9779 -20.9198 64.2904 11 0.6193 -0.2831 -0.1631 0.5037 -0.1341 0.7901 0.0127 -0.0186 -0.1407 0.0391 -0.032 0.1467 0.2311 -0.1685 0.0025 0.1768 -0.0467 0.033 0.131 0.0096 0.0748 -28.0145 -23.5188 79.1846 12 0.1202 0.0359 0.1157 0.0673 -0.0414 0.2124 -0.0021 -0.0548 -0.0506 0.0337 -0.0191 0.026 0.1162 -0.0173 0.0224 0.0945 0.0126 0.0522 0.0869 0.0146 0.128 -34.3269 -22.0241 50.0157 13 0.7856 -0.0168 0.2152 0.8663 -0.1396 0.5308 0.0177 0.0242 -0.0557 -0.017 0.0357 -0.0825 -0.088 0.0274 -0.0301 0.0498 0.0024 0.0474 0.0777 -0.005 0.0956 -12.1309 -10.8705 22.8855 14 0.1188 0.1539 -0.1629 0.2081 -0.2512 0.7374 0.0526 0.0178 0.1745 -0.0755 0.0374 0.0786 -0.0545 -0.0656 -0.0299 0.1835 -0.02 0.0765 0.0911 -0.0051 0.1699 -20.4097 7.7033 25.5701 15 0.5576 0.2762 0.3259 0.6567 -0.2502 0.6723 -0.043 0.0198 0.0828 0.0224 0.049 0.1606 -0.0778 -0.1686 0.0003 0.1759 0.0234 0.0531 0.1121 0.0222 0.1017 -27.1433 -2.2021 8.5736 16 0.2439 -0.0085 -0.3135 0.0136 0.0475 0.4998 0.0333 0.0621 0.1132 -0.0446 -0.0073 -0.0098 -0.0598 -0.0802 -0.0173 0.1019 0.0195 0.0557 0.1142 0.0273 0.1544 -33.3113 -3.784 28.6172 17 0.3627 -0.0591 0.2126 0.1957 -0.0607 0.5523 -0.0305 0.0476 0.0667 -0.0011 -0.0363 0.0142 0.0475 0.0313 0.0734 0.0794 0.0148 0.05 0.0866 0.0152 0.0911 -35.8077 -4.6384 46.1122
Refinement TLS group Show large table (4 x 17) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resseq 1:78)2 X-RAY DIFFRACTION 2 chain 'A' and (resseq 79:180)3 X-RAY DIFFRACTION 3 chain 'A' and (resseq 181:258)4 X-RAY DIFFRACTION 4 chain 'A' and (resseq 259:383)5 X-RAY DIFFRACTION 5 chain 'A' and (resseq 384:493)6 X-RAY DIFFRACTION 6 chain 'B' and (resseq 2:168)7 X-RAY DIFFRACTION 7 chain 'B' and (resseq 169:245)8 X-RAY DIFFRACTION 8 chain 'B' and (resseq 246:439)9 X-RAY DIFFRACTION 9 chain 'B' and (resseq 440:496)10 X-RAY DIFFRACTION 10 chain 'C' and (resseq 3:117)11 X-RAY DIFFRACTION 11 chain 'C' and (resseq 118:273)12 X-RAY DIFFRACTION 12 chain 'C' and (resseq 274:494)13 X-RAY DIFFRACTION 13 chain 'D' and (resseq 1:78)14 X-RAY DIFFRACTION 14 chain 'D' and (resseq 79:117)15 X-RAY DIFFRACTION 15 chain 'D' and (resseq 118:273)16 X-RAY DIFFRACTION 16 chain 'D' and (resseq 274:384)17 X-RAY DIFFRACTION 17 chain 'D' and (resseq 385:493)