[ccp4bb] difficult MR in R32(H32)

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

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From: Simon Phillips S {- dot -} E {- dot -} V {- dot -} Phillips {- at -} LEEDS {- dot -} AC {- dot -} UK
Date: 2008-11-11

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From: Charles Ballard charles {- dot -} ballard {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2008-11-12

Subject: difficult MR in R32(H32)
From: Shane Atwell satwell {- at -} SGXPHARMA {- dot -} COM
Date: 2008-11-11

I'm struggling with a molecular replacement. Its a kinase, for which we
have the structure in another spacegroup with a different ligand. The 3A
data processes in either C2 with ~12mol/asu or R3 with 8 or R32 with 4,
the later having higher but reasonable Rmerges. Low shells look good
(around 7%) The crystals themselves look classically rhombohedral. I
think R32 is the likely spacegroup.

Molecular replacement with either the entire kinase domain or the
C-terminal subdomain in C2, R3 and R32 has so far failed in phaser,
molrep and epmr. This is using the data in the hexagonal treatment
(H32). I've used phaser extensively, attempting to turn off clustering,
take top 1000 hits, and brute force rot/tran.

My questions are the following:

Does the hexagonal (H32) treatment of the R32 data introduce extra NCS
translational symmetries that could interfere with the MR? I don't think
this is the case, the H32 treatment should only introduce extra
crystallographic symmetries. (There still could be NCS translations
though since I have at least 4 molecules.)

Is there a molecular replacement package or setting that will do the MR
in true R32 and would this help?

Any other suggestions?

Thanks in advance.

Shane Atwell

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From: Charles Ballard charles {- dot -} ballard {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2008-11-12