Map doesnt fit model!

Herman Schreuder hermanschreuder at mmd.com
Tue Feb 27 02:51:30 EST 1996


On Feb 26, 10:35pm, Barani wrote:
> Subject: Map doesnt fit model!
> 
>   The protein is 18 KDa. Diffracts to 2.8 A. After homology
>   modelling, simulated annealing and positional refinements
>   the R-factor = 22.0 and R-free = 29.0.  The geometry is
>   good (0.01 and 2.0). The refinements are well behaved. No
>   water molecule added yet.
> 
>   But the electron density map is a NO NO fit with the model!!
> 
I had a similar experience with an enzyme-inhibitor complex where I
had 2.0 A data and isomorphous crystals. The statistics were excellent,
but the maps were garbage. It turned out that the data set used was
rather strong and all the strongest reflections were rejected by the 
defaults of FWIND (I did not put any FWIND statement, because I wanted
to use all reflections). Apparently, these defaults are quite low and
the solution was to add a statement like: fwind=0.1=10000000. After
including the strongest reflections as well, the maps looked excellent.

Herman Schreuder



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