First point - check that there really is no link between the N terminal
and C terminal - you need to use a CONTACT search or load them both into
coot or O or some graphics program which generates symmetry to look how
close the ends get. Any MR search can find any symetry equivalent.
Second point - have you tested both possible space groups P43212 and
P41212 - you can distinguish them from absences alone, but the
translation search should give a better answer in the correct SG..
Third point - phaser has certainly worked well for me with different
domains - you spilt your model at the hinge region and search for each
part in turn.
Fourth point - Jorge Navaza really developed AmoRe to search for FABs
and he maintained a library of models with different hinge regions -
there are dozens ofFABs available in the PDB.
Eleanor Dodson
Patrick G. Shaw wrote:
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Hello,
I have been working for some time on finding a molecular replacement solution
for an IGG receptor protein with little to show for it. My search model is a
previously published homologue of the protein that my colleagues and I now
suspect differs greatly with our crystallized protein about a central hinge
angle, despite 97% sequence homology between the two. Any attempts at molecular
replacement with the two domains treated separately result in a pdb with the
terminal ends pushed together instead of the ends that where severed about the
hinge region. This is probably due to the fact that the crystal is very tightly
packed and in high symmetry (P 43 21 2).
I was wondering if anyone knows of a way to perform molecular replacement
about a specific hinge region, I have heard rumors of a program that exists for
this very reason but have not been able to find it.
Thanks,
patrick
--
Patrick G. Shaw
Orville Lab
Georgia Institute of Technology
Institute for Bioengineering and Bioscience
315 Ferst Drive, Mailbox #8
Atlanta, GA 30332-0363
Tel: (404)434-2001 (Cell)
(404)894-4075 (Lab)
email: [EMAIL PROTECTED]
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