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

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: ligand refinemnet
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-04-02

Next message:
Subject: Vacancies at Diamond Light Source
From: "Hannon, TJ (Tim)" tim {- dot -} hannon {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2009-04-02

Subject: Re: Lowest resolution you can do MR with
From: Bjørn_Panyella_Pedersen bjopp {- at -} BIOXRAY {- dot -} AU {- dot -} DK
Date: 2009-04-02

I guess it depends on your criteria for success. We made a successful MR using
data to 8Å with a search-model with 20% identity covering 90% of the target. The
resultant phases gave a map where a few new 'blobs' could be observed. Not very
useful, but the MR-phases could be used to solve the HA substructure of a
derivative dataset we had using anomalous Fourier analysis. Thus the low-res MR
solution lead to the success of our _experimental_ phasing.
Especially pay attention on the quality of your low-res data. In our hands the
best dataset for MR was not the best dataset for later building the structure.
Test different programs (Phaser worked for us, but might struggle if you have
translational ncs (I think?)). Remember to play with the input parameters
(especially resolution cutoff, search-model, rms of search). Our MR first
succeeded after ~100 runs using different parameters (scripting is useful here!).

Good luck :)
-Bjørn

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.

--
Bjørn Panyella Pedersen, PhD
Postdoc

PUMPKIN, Centre for Membrane Pumps in Cells and Disease
University of Aarhus, Dept. Molecular Biology
Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark

Phone: +45 89425261
E-mail: bjopp@bioxray.au.dk
http://www.bioxray.au.dk

CCP4bb navigation

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

Previous message:
Subject: Re: ligand refinemnet
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-04-02

Next message:
Subject: Vacancies at Diamond Light Source
From: "Hannon, TJ (Tim)" tim {- dot -} hannon {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2009-04-02