Hi Zbyszek, thanks for your reply!
The scalepack log file gives the formula:
Chi**2 = SUM ( (I - I) ** 2) / (Error ** 2 * N / (N-1) ) )
which equivalent to the Jay Ponder's formula, with the important
addition, that sigma_avg and Iavg represent the average of all
_other_
What you're seeing is not necessarily pyrophosphate. The negative difference
density appears to concentrate around oxygen atoms most distant from the
protein (and perhaps around the putative phosphorous atom?). Some clues
might be obtained from e.g. the B-factor profile of the refined atoms. From
Could it be MPD (2-methyl-2,4-pentanediol)?
Cheers,
Charlie
Junyu Xiao wrote:
Dear all,
I am at the late stage of refining a 1.97 A structure. There is something
in the ligand binding pocket, and I am not sure what it is exactly. Since
this protein can potentially generate pyrophosphate from
