Based on eye-balling your map it looks to me that your grid spacing is about 0.5 A. The wavelength of your ripple is 4 grid spacings, and the ripple is right along the x axis. My guess is that you have a rogue reflection with index of h00 where h is about 2 A resolution.
How you are getting this in multiple data sets is a mystery to me, but I would concentrate on finding that reflection and figuring out why it is anomalously large. Start with the Fourier coefficients that went into calculating this map to find the exact value of h causing the problem and then track that reflection back through your Fcalc's and Fobs's. Dale Tronrud On 06/23/2013 09:57 PM, Peter Randolph wrote:
Short version: Hi, I'm working on what should be a straightforward molecular replacement problem (already solved protein in new space group), but my Fo-Fc map contains a peculiar series of alternating positive and negative peaks of difference density. I'm wondering if anyone has anyone seen this before? Sample images are attached and more background is below. More background: I had initially solved an /apo/ structure of my protein (from previous diffraction data in another crystal form), and more recently collected diffraction data for crystals of the protein co-crystallized with potential binding partners (small RNAs). All the datasets I've processed so far have the same spacegroup (P2(1)2(1)2(1)) and cell dimensions as the apo structure. I have tried two general approaches, both with the same initial steps of indexing / integrating / scaling in XDS, converting to MTZ format without R-free flags, then importing R-free-flags from the (previous) apo structure's MTZ. I would then run "phenix.refine" for initial rigid-body refinement using the apo-model and the new mtz to see if there were signs of any new positive density corresponding to bound ligands. While the 2Fo-Fc map fits the apo protein 3D model perfectly, the Fo-Fc map shows bands of alternating positive and negative density running throughout the structure. What's odd is that these 'bands' appear to be systematic rather than random (please see attached image), and aren't located anywhere that a binding partner could bind, leading me to suspect they may be artefactual (these bands actually run through the body of the protein, so one possibility is that the b-strands are off-register by a multiple of a peptide unit?). If I use the same mtz file and structural model, and instead do molecular replacement with phaser, I see the same issue. I've tried this workflow with a couple of datasets and using P222 as well as P2(1)2(1)2(1), and each time I see the same issue of spurious(?) bands. Any help or advice would be much appreciated, especially if anyone has seen anything like this? Thanks a lot, Peter Randolph -- Peter Randolph PhD Candidate Mura Laboratory Department of Chemistry University of Virginia (434)924.7979
