tl;dr: My data has native Patterson peaks but no tNCS; I can solve the structure and refine to reasonable R/Rfree, but much of the map is poor quality.
More details: I have crystallized a heterodimer of Z domains (small three-helix bundles, like pdb id 8DA3) in a few different crystal forms that all diffracted in the 2-2.5 Å resolution range, though in different space groups and different asymmetric unit volumes. I’ll focus on the most successful crystal, space group C2221 a = 39.9 b = 74.8 c = 147.2 Å. All of these data sets have native Patterson peaks (for the crystal in question, there are peaks at [0.5, 0, 0.034] and [0.127, 0, 0.131] that are both 23% of the origin height) but tNCS search mode in phaser failed. Turning off tNCS and searching separately for chain A and chain B of the heterodimer, I am able to find two heterodimers – that are not related by simple translation. TFZ for the first heterodimer is 14.6, which decreases to 13.1 after finding the second heterodimer, though LLG increases. Electron density for the first heterodimer (AB) is very good, with easily identifiable side chains. Density for the second heterodimer (CD) is pretty dodgy; though some side chains are identifiable, chain D has tube-like helices. Using NCS restraints, I’m able to refine to Rfree/Rwork 0.27/0.24, but can only place 3 water molecules (with 240 protein residues in the ASU). All of this suggests to me that there must be some kind of modulation of my reflection intensities, though nothing is apparent to me in studying raw or pseudoprecession images. If possible I’d like to figure out how to correct it, but barring that I would be happy to describe it and possibly relate it to my structure. I’m at a loss for the next step, though, and would appreciate any advice from the community on how to approach this. Best wishes to all, Kevin -- Kevin M. Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
