I have two bits of advice. 1. If the SA omit map for the ssDNA is "really bad", perhaps you should reconsider whether your model is a faithful representation of the experimental data.
2. You could use anomalous difference Fourier analysis to locate the P atoms of the DNA backbone. We did this for ssDNA bound to a Fab using a data set collected at wavelength=1.74 A. See Figure 3 of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516951/ John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: [email protected]<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html On Nov 4, 2013, at 10:42 AM, Matthew Franklin <[email protected]<mailto:[email protected]>> wrote: Hi Deng - Can you tell why the reviewer was asking for the SA-omit map? Is there some doubt about the conformation of your ssDNA, or even whether it is present in the first place? Is there a question about the sequence, or the sequence register (which nucleotides go in which positions)? Even a poor-quality map should let you locate the phosphate backbone of the DNA. This should convince most reviewers that the DNA is present and in the general position you have modeled. You can't resolve concerns about nucleotide base position or conformation without a better quality map. I imagine that you built the protein model first during your structure determination, and only added the ssDNA later in the refinement. If this is correct, you could present the maps from the last refinement cycle before you added the DNA. This is even less model biased than what the reviewer wants. Hope that helps, Matt On 11/4/13 1:36 AM, dengzq1987 wrote: Dear all, Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A，but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map? Thank you! Bests, zq Deng 2013-11-04 ________________________________ dengzq1987 -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
