Re: [ccp4bb] Lowest resolution you can do MR with
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: bj...@bioxray.au.dk http://www.bioxray.au.dk
Re: [ccp4bb] Lowest resolution you can do MR with
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] Lowest resolution you can do MR with
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.
Re: [ccp4bb] Lowest resolution you can do MR with
If you look at the molecular replacement search parameters, you will find that the rotational and translational searches can be done at 4 Angstrom or lower values assigned to the 'high resolution' values. So the real worry in your case, in all likelihood, is not whether MR will work for 3.6 Ang resolution data. The greater worry is as to how much model bias gets introduced at that resolution and as to how well one can refine the model only based on the phases from molecular replacement. I can't tell from your description if you have DNA in your search model or not. But If you get a molecular replacement solution and if at the least, some bits of your DNA molecules are ordered, you will see big bloopers of density that will correspond to the phosphate molecules. The density for sugars and base-pairs may or may not be well defined in the initial stages. Raji On Mar 30, 2009, at 12:25 PM, 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.
