Hi, Yi,
Take a look at our paper:
Acta Crystallographica Section D: Biological Crystallography D60, 447-452
You might get some input from it. As suggested by other crystallography
guru,
pseudosymmetry(C F I centered) definitely need be considered in your case.
Regards
Yanming
On Thu, 1 Jun 2006, Yi Xue wrote:
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Hi, all:
thanks a lot for all your responses.
The space group is P212121, a 38.43A, b 41.619A, c 44.219A.
The solvent content is 31%.
When I integrated the data, the prediction perfectly conformed to the
observed pattern.
Since all axes have different lengths, at least the twinning could not be
merohedral.
Besides, after data integration and scaling, I checked the data, and it
showed clear systematic absence for all axes.
more suggestion?
Yi
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of
David Schwefel
Sent: Thursday, June 01, 2006 4:00 AM
To: [email protected]
Subject: Re: [ccp4bb]: Rfree can not be decreased
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Hey Yi!
I had almost the same problems with a twinned crystal... the solution was
refinement with SHELXL using the TWIN and BASF commands. the only thing you
have to find out is the symmetry relationship between the twin domains (twin
law). Look for another indexing possibility for your crystal, the symmetry
relationship between this space group and your original one would be the
twin law. There is also a lookup table for possible twin laws of
merohedrally twinned crystals on the ccp4 homepage
(http://www.ccp4.ac.uk/html/twinning.html).
The BASF command defines the twin fraction, the relative proportion of the
twin domains, an estimate is given by SFCHECK, but it will be refined by
SHELXL. Using this refinement procedure decreased R/Rfree >15% in my case!
good luck, david
-------- Original-Nachricht --------
Datum: Wed, 31 May 2006 17:36:21 -0500
Von: Yi Xue <[EMAIL PROTECTED]>
An: <[email protected]>
Betreff: [ccp4bb]: Rfree can not be decreased
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Hi, all:
I tried to solve a protein structure by molecular replacement. The apo
form is already solved, I crystallized it with Cu(II). The data diffracted
to 1.6A, the highest resolution shell has more than 80% completeness, R is
43%.
I used phaser to find the MR solutin ,then used Refmac to do rigid body
refinement, and restrained refinement. I adjusted weighing factor to keep
chi^2 exactly 0.01. After these steps, R is around 0.30, Rfree is about
0.37.
Then I fed all the data to arp/warp, it showed that while R decresed,
Rfree increased, and finally, Rfree is around 40%.
I tried to manual build the model, however, I found that most density
were unambigously assigned. I only need to do some small adjustments,
these
minor adjustments did not improve R factors a lot.
All suggestions are highly appreciated.
Best regards
Yi
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