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

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- July 2007 <-- 31 July 2007

Previous message:
Subject: Post-doc: EM Model Refinement Methods Development; Portland, OR.
From: "Michael S {- dot -} Chapman" chapmami {- at -} OHSU {- dot -} EDU
Date: 2007-07-31

Next message:
Subject: problems with restrained refinement in refmac5
From: "Nagatani, Ray" ray {- dot -} nagatani {- at -} UCSF {- dot -} EDU
Date: 2007-07-31

Subject: how to bring back the missing density for half of the structure
From: Eric Liu supererictaoranliu {- at -} GMAIL {- dot -} COM
Date: 2007-07-31

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

CCP4bb navigation

CCP4bb <-- 2007 <-- July 2007 <-- 31 July 2007

Previous message:
Subject: Post-doc: EM Model Refinement Methods Development; Portland, OR.
From: "Michael S {- dot -} Chapman" chapmami {- at -} OHSU {- dot -} EDU
Date: 2007-07-31

Next message:
Subject: problems with restrained refinement in refmac5
From: "Nagatani, Ray" ray {- dot -} nagatani {- at -} UCSF {- dot -} EDU
Date: 2007-07-31