Re: [ccp4bb] Low resolution data with substrate

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Fwd: crystallisation robot
From: Jochen Muller-Dieckmann jochenmd {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2008-04-15

Next message:
Subject: Revise
From: sajid akthar b_sajid_ali {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-04-15

Subject: Re: Low resolution data with substrate
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-04-15

yang li wrote:

> Hi All,
> We have several substrate-soaked data with resoltuion from
> 3.1~3.6A, after refinement
> with the native structure, the rfree are in the range of 0.29~0.34. We
> found in the expected
> active site there do have extra densities, but not very clear. In some
> chains the densities
> are big while in other chains very small. For some good extra
> densities can fit the substrate
> in but cannot specify the accurate atom positions. And the map
> densities seem not very convictive(low resolution or bad refinement?).
> This is a relative big structure, I think it would be difficult to
> rebuild it in such low resolution. We also has tried to use the sulfur
> anomalous signal in the substrate in 1.54A, but it failed since all
> the sulfurs in the model have no signal. So anyone has some methods
> to make the density better or make sure whether it has substrate
> soaked in?
>
> Thanks!
>
>

I assume you already tried composite omit maps in CNS - if not that
would be a possibility.
If you're in desperate mode you can enhance your density magically by
using the program GraphEnt, depending on the number of reflections you
have you might have to recompile the program. In one of my trickier
cases I was able to actually build a peptide into a map obtained through
GraphEnt and then further refined it in Refmac.

Good luck !

Juergen

P.S. alternative get better diffracting crystals - e.g. analyse your
crystal contacts and do some favourable cloning.

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Fwd: crystallisation robot
From: Jochen Muller-Dieckmann jochenmd {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2008-04-15

Next message:
Subject: Revise
From: sajid akthar b_sajid_ali {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-04-15