Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution
Dear all and specially Eleanor, Thank each and everyone who responded to my query. All your suggestions made me to think in all possible dimensions. I have good news to share with all of you. Balbes gave me marginal solution with model which had 29% sequence identity. At present I am doing model building and refinement with R-free 47 and R-factor 45. My special thanks to Garib…. (I don’t think I should mention once again for what ..) and his web server. Wish you a happy new year to all the members. With regards somu From: Eleanor Dodson To: Meetmr Ss Cc: CCP4BB@jiscmail.ac.uk Sent: Tuesday, December 30, 2008 2:04:24 PM Subject: Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution Meetmr Ss wrote: > Dear all, > > I struck with MR problem. MY target has 76% sequence identity with the model. > I tried Phaser, AMoRe and Molrep. None of them gave me satisfactory solution. > If you have any suggestions and or New programs I would like to try. > Thanks > somu > > > > Is your space group correct? Eleanor
Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution
Meetmr Ss wrote: Dear all, I struck with MR problem. MY target has 76% sequence identity with the model. I tried Phaser, AMoRe and Molrep. None of them gave me satisfactory solution. If you have any suggestions and or New programs I would like to try. Thanks somu Is your space group correct? Eleanor
Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution
I had the same problem with an even higher %identity once (>80%), eventually resorted to SIRAS phasing with a mercury compound, and I found a case of domain swapping creating a novel dimer interface. Flip
Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution
Hi Somu, Here are a few questions which might help: Are you sure about about your space group? Is another lattice/symmetry possible? Is twinning possible? Have you tried all possible space groups in MR? Have you tried different resolution ranges (e.g. all data, cut low resolution at 15 A, cut high resolution at 3 or 4 A)? Do you have models from other homologs? You can try them individually or input everything you have in phaser. Did you input 76% sequence identity in phaser? Try with lower values (larger difference between MR model and structure) or higher rmsd values (1.0, 1.2, 1.5) instead. Good luck, christian Meetmr Ss wrote: > Dear all, > > I struck with MR problem. MY target has 76% sequence identity with the > model. I tried Phaser, AMoRe and Molrep. None of them gave me > satisfactory solution. If you have any suggestions and or New programs I > would like to try. > > Thanks > somu > ___ 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 ___
Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution
I struck with MR problem. MY target has 76% sequence identity with the model. I tried Phaser, AMoRe and Molrep. None of them gave me satisfactory solution. If you have any suggestions and or New programs I would like to try. that is odd. at 76% SI mol. repl. should normally be a breeze. possibilities: - does your protein have multiple domains? if so, maybe their relative orientation differs - try searching with the individual domains - is there a problem with the data perhaps? run it through xtriage to check - are you sure you have crystallised the right protein? don't laugh - been there, done that, got the PDB entry (2CDS was supposed to have been 1CBS... no wonder my 3 zillion mol. repl. trials didn't work - until i eventually recognised the cell constants of tetragonal lysozyme... i learned a lot about mol. repl., though) good luck! merry x-mas/hannuka/flying-spaghetti-monster-mas/wednesday everybody! --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
[ccp4bb] MR- Problem-76 % seqeunce identity-no solution
Dear all, I struck with MR problem. MY target has 76% sequence identity with the model. I tried Phaser, AMoRe and Molrep. None of them gave me satisfactory solution. If you have any suggestions and or New programs I would like to try. Thanks somu
