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Re: [ccp4bb] how to bring back the missing density for half of the structure
 

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CCP4bb <-- 2007 <-- August 2007 <-- 01 August 2007
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Subject: Re: how to bring back the missing density for half of the structure
From: Eric Liu supererictaoranliu {- at -} GMAIL {- dot -} COM
Date: 2007-07-31 		Next message:
Subject: difference density ripples around Hg atoms
From: Klemens Wild Klemens {- dot -} Wild {- at -} BZH {- dot -} UNI-HEIDELBERG {- dot -} DE
Date: 2007-08-01


Subject: Re: how to bring back the missing density for half of the structure
From: "Fan, Hai-fu" fanhf {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN
Date: 2007-08-01
Dear Eric,

For your question 2, the following paper provides some examples:

Acta Cryst. D63, 793-799 (2007).

In one of the examples, there is shown a partial model from Phaser
containing ~20% residues in the ASU can be extended to more than 90% of the
ASU by the iteration of ARP/wARP-OASIS-DM. Detailed examples and scripts on
using OASIS can be found on the download page of

http://cryst.iphy.ac.cn

Regards,

Hai-fu


On 8/1/07, Eric Liu wrote:
>
> Hi All,
> I would like to get some help from here for a data set I recently worked
> on. I have been working on a new kinase data set which does not have a close
> homolog. The data was collected to 2.1A resolution in space group P212121
> however the difference between a and b is only 0.5A. If I index the data
> as P4, Rmerge is increased from 13% to 39%. I used the most close homologs
> which have about 37% sequence identity as search model for molecular
> replacement and it seemed I have got the solution by using Phaser with only
> the c-terminal part of the search model and also a long loop removed. After
> changed the different residues back to the target protein, the structure was
> refined to Rfree/R 46% and 43% to 2.1 A resolution. The existing
> c-terminal structure has well defined density except 25ish residue at the
> very c-terminal end doesn't have well connected density. Current
> model contains about 50% of overall target residues. I can see some extented
> difference density for several residues going to the N-terminal part and
> also extented density for the C-terminal loop for several residues. I also
> see tones of not well-conncted difference density in the N-terminal region.
> There was no sever clashes between molecules after mount all
> symmetry related molecules. My question is the following:
>
> 1. Have I got the correct solution for the molecular replacement?
> 2. How can I bring back the missing density for the N-terminal residues
> and the loop region?
>
> I would really appreciate any inputs or suggestions.
>
> Eric
>
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