[ccp4bb] High R factors in Orthorhombic Space Group

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Bad geometry for alt. conformation refined in Refmac5
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-12-03

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Subject: Re: High R factors in Orthorhombic Space Group
From: mjvanraaij mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2009-12-03

Subject: High R factors in Orthorhombic Space Group
From: Robert Radford rradford {- at -} UCSD {- dot -} EDU
Date: 2009-12-03

Hello-

I am working up a data that is giving me unacceptable high R factors.

I am solving a data set that is good to ~ 2.3 Å using molecular
replacement based on a previously crystalized variant. The maps look
good with all the density fitting well to my model. I originally
worked up the data using PHASER for the molecular replacement. It
searched all alternative orthorhombic space groups and found a single
solution in P2(1)2(1)2 but that only gave me final R factors of (Rwork
= 0.26 and Rfree = 0.32) Next I went back and tried to work the data
up in a different space group. Thus far I have tried P21 and P1. Both
these space groups give me essential the same final statistics (~Rwork
= 0.26 and Rfree = 0.32). Furthermore, the solution looks the same,
the only change being the number for monomers in the asymmetric unit
(1, 2, 4 for P21212, P21 and P1 respectively) The diagnostics don't
indicate that the crystal is twined and the data set looks good (i.e.
the spots are nice and well separated)

The unit cell dimensions for the three cases as

P1: a = 34.55 b = 46.95 c = 88.56, alpha = 89.94, beta = 90.03
gamma = 89.99
P21: a = 46.91 b = 34.52 c = 88.47, alpha = 90 , beta = 90.03 gamma
= 90.0
P21212 a = 88.44 b = 34.51 c = 46.89, alpha = 90.0, beta = 90.00
gamma = 90.0

One possible complication is that the biological unit is dimeric with
2 fold symmetry. The 2 fold symmetry axis for the protein appears to
be sitting on a 2-fold crystallographic axis.

Any suggestions?

Thank you in advance.
Robert
________________
Robert Radford

Graduate Researcher
Dept. Of Chemistry
UC San Diego

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Bad geometry for alt. conformation refined in Refmac5
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-12-03

Next message:
Subject: Re: High R factors in Orthorhombic Space Group
From: mjvanraaij mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2009-12-03