Re: [ccp4bb] Lowest resolution you can do MR with

- Protein crystallography

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

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From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-04-01

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Subject: Re: Lowest resolution you can do MR with
From: Christian Biertuempfel biertumpfelc {- at -} NIDDK {- dot -} NIH {- dot -} GOV
Date: 2009-04-01

Hi,
I cannot really answer what the lowest resolution for MR is but I have
been successful with 4 A data for a protein-DNA complex and so I
encourage you to try your 3.6 A data set. Of course, it also depends on
the quality of your data, in particular how well/how many low resolution
reflections were measured, solvent content and your search model.

In my case, I have used only protein as the search model (45% of the
molar mass was missing) to reduce model bias and to avoid trouble with
different DNA conformations (deviating from ideal B-DNA).
The obtained MR solution gave a correct packing (for protein) with a lot
of space for DNA. The resulting electron density map showed clear
density for protein but it was very noisy apart from that. I have used
density modification (solvent flipping) in CNS to increase the contrast
of the map and it brought out a signal for DNA (solvent content was
65%). As Raji pointed out, have a look for the phosphate backbone or
some density in a helical arrangement. Most probably, you will not be
able to resolve individual bases.

Good luck,
christian

Muthiah wrote:
> What is the lowest resolution one can try to do molecular replacement
> with? I have a 3.6 angstroms resolution data for a protein-DNA complex
> and wondering whether I can try MR to see the density for DNA.

_______________________________________________________________________

Dr. Christian Biertümpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________

CCP4bb navigation

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

Previous message:
Subject: Re: Eleven plausible phasing elements remain unused
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-04-01

Next message:
Subject: curvature of a helix
From: peter hudson peter {- dot -} hudson {- dot -} peter {- at -} GMAIL {- dot -} COM
Date: 2009-04-01