Re: [ccp4bb] Very weird

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CCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007

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Subject: protease cleavage sites
From: Rene Frank rf3 {- at -} SANGER {- dot -} AC {- dot -} UK
Date: 2007-03-05

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Subject: Re: Solubility of ligands - Summary
From: "Ibrahim M {- dot -} Moustafa" I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-03-05

Subject: Re: Very weird
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-05

It seems very odd..in fact almost impossible. You still have 3 correct
molecules
I wonder if there is some error in the coordinate file?
Errors I make are:

leaving and end record, between 2 parts. - many programs stop
reading coordinates at the first END

leaving CRYST1 and SCALE cards in the middle of the file..
Getting the CRYST record wrong somewhere - REFMAC does not seem to
check that the cell dimensions are consistent

Eleanor

Yanming Zhang wrote:
> Dear all,
>
> I am sorry to trouble you again because I am facing a very weird
> situation:
>
> Three copies from Phaser are the right solutions based upon:
> 1, Rfree 42% R 39%
> 2, No packing clash
> 3, The packing within the 3 makes good sense
> 4, Density evenly distributed among the 3 copies even without NCS
>
> Then fix these 3, asking Phaser to find one more (here I adopt the
> strategy one copy at a time). Phaser did find one more, So now I have
> 4 copies in total.
>
> Using the phase calculated from the previous 3 copies(because Rfree
> 42%), the 4th copy can exactly match one junk of the density, even the
> side chain matchs, demonstrating the 4th copy is correct.
>
> Checking the crystallographic packing, The density which the 4th
> occupies, is an extra density which did not account for by the
> previous 3 copies or their symmetry mates.
>
> No Clash exists
>
> Then I use the 4 copies to do the refinement, forseeing that there
> will be a huge Rfree drop from 42% because I account for the extra
> density using the 4th copy. BUT TO MY SURPRISE, THE RFREE INCREASE TO
> 65%.
>
> Can you teach me what is going wrong? Thank you
> Yanming
>
>

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007

Previous message:
Subject: protease cleavage sites
From: Rene Frank rf3 {- at -} SANGER {- dot -} AC {- dot -} UK
Date: 2007-03-05

Next message:
Subject: Re: Solubility of ligands - Summary
From: "Ibrahim M {- dot -} Moustafa" I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-03-05