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[ccp4bb]: Re:
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sameeta bilgrami wrote:
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> dear all,
> i have a dataset in p212121 upto 2.9 A
> resolution and 78% ....(the crystals die in the beam)
> ......while i am trying to produce better crystals i
> tried MR on the present dataset....i got the solution
> and it refined quite nicely in refmac with a matrix of
> 0.06 untill and unless i did not do any major changes
> in the chain, except for side chain .... but at about
> R of 23.8 and freeR of 26.3...i could see quite a lot
> of changes in the main chain (many new densities had
> apeared which required moving whole amino acids a
> little)...when i did thoe changes my R dropped to 22.4
> but my freeR increased to 29.0 .... now my questions:
> 1) why is my freeR increasing....can that density
> should not be trusted and therefore those changes not
> made....
> 2) what all precautions one should take (or in another
> way what all problems can come) if we have an
> incomplete dataset....
> thanx in advance for all the suggestions..
> sameeta bilgrami
>
While you are rebuilding ( and espec at 2.9A ) the Free R would be
expected to be > 30% I would think - if it isnt there is something
suspicious!
Do you have more than one molecule in th asymmetric unit? There are
ways to corrupt FreeR sets if there is pseudo-symmetry which may be
broken after rebuilding.
Or maybe the geometry is now much less tightly restrained?
Remember that a FreeR is an indicator only - there is no requirement to
achieve a certain limit, and before your model is complete and correct
it has no particular absolute relevence.
Eleanor
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- From: sameeta bilgrami <sameeta_b@yahoo.co.in>