Thanks to all that responded. I sorted this out.
It all appears to stem from the C2->I2 conversion. Forcing everything in
processing to stick with C2 fixes all the issues!
Thanks again,
--paul
On 11/03/2016 12:39 PM, Paul Paukstelis wrote:
> CCP4BB,
>
> I posted some time back about a DNA oligonucleotide structure we were
> working on. I had difficulty phasing it despite strong signal from
> bromines, but finally managed to get reasonable enough maps from a few
> datasets to build, only to find that despite the density looking quite
> good, it simply wouldn't refine past R/Rfree of around 28/32. With
> help from ccp4bb it began to become clear that this might be a
> candidate for a lattice with translocation defects.
>
> I had my student make a variant in which two 3' nucleotides that
> weren't involved in base pairing contacts were removed. This
> crystallized under the same conditions in a different space group and
> was now diffracting to ~1.0 A (from about 2.2 in the previous space
> group). Images overall looked good, though we collected on some
> crystals that clearly had more than one lattice that made indexing
> more difficult. The best looking data still had some tails on spots,
> but was easily indexed in C2, which Pointless quite happily changed to
> I2 to minimize the beta angle. There are no clear alternating
> strong/weak intensities. Phaser finds a strong solution using the
> previously built dimer, but notes a 25% over origin peak in native
> Patterson. Maps look very good, though after the first round of
> refinement it is apparent that there is another dimer in the ASU, but
> it is clearly overlapping the first. If I'm not mistaken, all these
> clues suggest lattice translocation defects. Question 1: any thoughts
> on how likely it would be for a molecule to intrinsically pack in such
> a way that it results in lattice translocation defects?
>
> I thought it would be worthwhile pressing on given the high resolution
> it would be possible to do grouped occupancy refinement of the dimers
> without taking too huge a hit in observation/parameters. Refinement
> with refmac using occupancy groups leads to a best R/Rfree of 18/24,
> though geometry could be better in some spots. Curiously, refmac (or
> phenix.refine) in the PDB header reports only 50% completeness in the
> resolution range, though all the data reduction and analysis (aimless,
> xtriage) report 99% completeness. Question 2: Why is this? Phenix
> logfile says something about removing about half the reflections as
> systematic absences. I have been working with everything in I2 after
> Pointless switched it over.
>
> Question 3: Any other suggestions on how to proceed with refinement in
> a case like this? My gut instinct tells me that it would be better to
> not do intensity correction due to the high resolution, but perhaps
> that's something to pursue?
>
> Thank you in advance.
>
> --paul
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