change in unit cell parameters and difficult MR

From: intekhab alam
Date: 27 February 2012 06:44

Hi all

I have collected 2 datasets; one for the native proteins (2.3Å resolution) while other is for a protein-protein complex (3.5Å resolution). The unit cell parameters for the native are a=120, b=196, c=109, a=g=90, b=114, while for the complex data it is a=122, b=197, c=300, a=g=90, b=93. I have successfully got a MR solution and refined the native dataset with 3 monomers in the asymmetric unit. Analysis of the protein complex dataset shows 41% pseudo translation and so far there is no success in molecular replacement for this dataset. Can anyone please suggest me ways to solve this problem. i already have tried different templates like monomer, dimer, trimer, tetramer etc with truncations of loop region. i am using phaser as well as molrep programs.

Regards
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INTEKHAB ALAM

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From: Eleanor Dodson


 Well, there is an obvious relation between cell dimensions - what is the translation vector you find at 41%

You say the native structure has 3 monomers - I would send those coordinates to the PISA application at the EBI, and see what the interfaces are and make sure you are using closely packed search models - eg you may find there is a closely packed trimer which is built using symmetry equivalent molecules to your native solution..

Hard to answer without more information though.
ie space group, relative size od protein and complex etc..
Eleanor

Professor Eleanor Dodson