Hi Todd, in addition to all other suggestions, here is some basic sanity check that you can do in no time:
- how the R-factor vs Resolution plot looks like? - did the bulk-solvent correction was done right (what are k_sol and B_sol values)? - plot the scatterer graph Fobs vs Fmodel and see if there are severe outliers? Did removing them changes the map? - how the Data completeness vs Resolution plot looks like? - how POLYGON plot looks like? The answers will give some food for thought, and probably will invite some more more specific suggestions. All the best! Pavel. On Fri, Jan 28, 2011 at 12:29 PM, Todd Geders <ged...@strayxray.com> wrote: > Greetings CCP4bb, > > *Short version: > > Very noisy difference maps from a crystal with extremely high solvent > content, seeking advice on how best to handle such high solvent content to > eliminate noise in difference maps. > * > *http://strayxray.com/images/coot.jpg* > > Long version: > > I'm having trouble with a 3.0Å dataset from a crystal with 80% solvent > content. The space group is P4132 and I'm quite confident the high solvent > content is real (there is a species-specific set of helices extending into > the solvent channels that appears to prevent tighter packing). > > I was able to get a MR solution using a structurally related enzyme, but > the difference maps are terribly noisy (see link). There are lots of > negative density in empty spaces between well-defined 2Fo-Fc electron > density. > > http://strayxray.com/images/coot.jpg > > The 2Fo-Fc density actually looks fairly good. The initial MR maps had > clear density correlating to the sequence differences between the MR model > and the crystallized protein. After fixing the model as best I could, the > refinement statistics are R/Rfree of 27.5/30.3 with a data/parameters ratio > of 1.7. > > The mosaicity ranges from 0.15-0.3, data were collected with 0.5° > oscillations and 180° of data were collected. > > http://strayxray.com/images/diffraction.jpg > > Since the crystals appeared to suffer from radiation decay (based on > scaling statistics), I only use the first 40° of data (which still gives > around 8-fold redundancy). Using more minimal wedges of data or more data > does not noticeably make better or noisier maps. > > Any advice on improving the maps? Could the noisy maps be due to the > extraordinarily high solvent content? > > I'd appreciate any advice or comments. > > ~Todd Geders >
