Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

[ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 10 May 2007
Previous message:
Subject: Re: rmsd calculation. .
From: "Kerr, Iain" Iain {- dot -} Kerr {- at -} STJUDE {- dot -} ORG
Date: 2007-05-10 		Next message:
Subject: Re: rmsd calculation. .
From: Miguel Ortiz Lombardia molatwork {- at -} YAHOO {- dot -} ES
Date: 2007-05-11


Subject: Molecular Replacement issues with a WD-40 7-bladed beta propeller
From: Scott Coyle scoyle79 {- at -} BERKELEY {- dot -} EDU
Date: 2007-05-10
Hello,
I'm an undergraduate and recently crystallized and obtained 2.9A
diffraction data for a protein which is predicted to fold into a WD40
7-bladed beta-propeller structure (which has been crudely verified by
cryo-EM by another lab). The space group appears to be I4(1) with
unit cell parameters 118.936 118.936 85.456 90.000
90.000 90.000. Using a number of different search models (which I
trimmed and aligned to my protein's sequence using Chainsaw) I have
obtained a number of MR solutions placing 2 molecules in the AU with
Phaser with high Z-scores (ranging from Z=9 to 12) that seem to pack
together nicely, so I was hoping to use this technique to solve my
structure. However, the initial Rfree for my best solution is
relatively high (0.49) and all attempts to refine the structure
result in the Rfree blowing up almost immediately. This makes me
worry that the maps I'm generating may be too model-biased to use to
generate a solution. I've tried using Prime and Switch to remove
model bias but the resulting map looks worse than the starting map.
As the predicted structure possesses so much radial symmetry (7-
fold), I'm worried that my MR solutions will never be oriented
correctly enough for me to be able to build a model. If anyone has
any suggestions for tackling this kind of molecular replacement woe,
I would greatly appreciate it. Otherwise I guess I'll just plan to
collect experimental phasing information sometime in the near future.

I'm not sure if this is the right place to be asking this question,
perhaps you guys could direct me elsewhere.

Thanks!
-Scott

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 10 May 2007
Previous message:
Subject: Re: rmsd calculation. .
From: "Kerr, Iain" Iain {- dot -} Kerr {- at -} STJUDE {- dot -} ORG
Date: 2007-05-10 		Next message:
Subject: Re: rmsd calculation. .
From: Miguel Ortiz Lombardia molatwork {- at -} YAHOO {- dot -} ES
Date: 2007-05-11


ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd