or could it be in part a statistical effect, if the scala-map is
flatter, the differences near the ligand stand out more (i.e. are at
higher level relative to sigma), while they are really the same height
in absolute (electron-density) terms?
Mark van Raaij
http://web.usc.es/~vanraaij/
On 16 Sep 2008, at 18:56, Kay Diederichs wrote:
> Hi Sabine,
>
> difficult to say anything without knowing more about your procedures
> and data. I would not exactly consider the difference between
> 20.9/24.8 and 21.6/26.1 as tiny.
> One question - which procedure did you use to go from XDS_ASCII.HKL
> to the mtz-file for SCALA? There are two different ways described at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA
> but there may be other ways ...
> What are the high-resolution R-factors of the model against the data
> for (1) and (2)?
> Maybe you could trace back the difference to a few high-intensity
> reflections that were rejected as misfits by XSCALE, or as Wilson
> outliers, using REMOVE.HKL, by you?
> Are the positive and negative blobs at chemically sensible places,
> i.e could the positive ones be waters and the negative ones mis-
> placed model?
>
> best,
>
> Kay
>
> Sabine Schneider schrieb:
>> Hello everyone,
>> I am puzzled about differences I see when I refine the very same
>> structure against data processed with xscale or scala.
>> I got data to 2.55A from a protein-ligand complex. The data were
>> processed with xds/xscale (1) or xds/scala (2)
>> Free R was imported from a previously solved structure with a
>> different ligand, first to (1) and from there to (2).
>> After MR and refinement (Refmac/Phenix), I get some difference
>> density peaks (a bit pos and neg), near the ligand when I refine
>> against (1) and it converges more or less around R/Rfree of 20.9
>> and 24.8. I do not get these pos and negative density blobs when I
>> refine the same coordinates against (2), with a tiny bit higher R/
>> Rfree of 21.6/26.1?
>> So the data processed with scala, where I get slightly better
>> refinement statistics, I end up with some pos/neg density peaks.
>> They don't show up when I apply a high resolution cut-off of 2.65A
>> during refinement.
>> Symmetry is orthorhombic and the statistics are OK (Rsym 0.09 and
>> 0.38 in highest shell, redundancy ~5, I/sigI =1.9, mean I/sigI =
>> 5.2 ) and in both files appear to be more or less the same number
>> of reflections.
>> I also did simulated annealing, omitting the region around the
>> ligand in a 15A radius and the density is nicely coming up. But it
>> doesn't make a difference: after refinement I always end up with
>> the result as discribed above? And there isn't really a difference
>> between the two structures in the end.
>> Has anyone an idea whats going on?
>> Sabine
>
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