Dear all,<br><br>I am refining a protein-DNA complex structure at 2.9A resolution. The R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA is not well refined. Some sugar puckers are not right. The distances between some base-paired bases are kind of short (~2.5A). I&#39;ve tried including a reference model for the DNA, or including a cif file, and I&#39;ve also tried to turn on the secondary_structure_restraints.... nothing worked. I must have not done it in a correct way. But how to do it? And how to deal with sugar puckers?<br>
In refmac, I can set the distances between bases during the refinement, so there must be a way to do it in phenix as well?<br><br>Any advice is welcome.<br>Thanks!<br><br>Xun<br><br><br><br>-- <br>Department of Molecular and Structural Biochemistry<br>
North Carolina State University<br>