Yes, Eleanor D. is right. I had a similar experience. MR did not provide me the solution with monomeric protein. However, when i used dimer as a search model, it appeared to be a low-hanging fruit afterwards. May be you have a similar situation, there are very less possibilities to explain othewrwise. I assume that you considered removing the flexible loops and variable side chains of the homologous protein before declaring it as a search model.
All the best Zaigham On Nov 1, 2016 06:24, "Eleanor Dodson" <[email protected]> wrote: > With such a lot of molecules, I would check for oligamers. Look at the > MOLREP self rotation - is there anything obvious? Send the*.ps if you like > and I can comment. > > And do the models form oligimers? If so search with that.. > Eleanor > > And as Randy says - try PHASER .. > > > On 31 October 2016 at 21:30, Randy Read <[email protected]> wrote: > >> Dear Alex, >> >> We’ve had very good luck using Phaser to place large numbers of copies of >> good models. It’s in this kind of case where the increased sensitivity of >> the likelihood approach really helps. I would suggest trying the different >> choices of model as alternatives, and you might also want to make an >> ensemble in which loops that deviate among the different models have been >> trimmed off. >> >> If you need more advice on how to do this, you can get in touch off-line. >> >> Best wishes, >> >> Randy Read >> >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> Wellcome Trust/MRC Building Fax: +44 1223 336827 >> Hills Road >> E-mail: [email protected] >> Cambridge CB2 0XY, U.K. >> www-structmed.cimr.cam.ac.uk >> >> > On 31 Oct 2016, at 18:16, Alex Lee <[email protected]> wrote: >> > >> > Hi All, >> > >> > I have a protein which contains 72 amino acids. The crystal of this >> protein diffracts to 2.5A with SG P31 (CELL Dimension 65.9590 65.9590 >> 164.3900 90.0000 90.0000 120.0000). Pointless indicates no twinning. >> > >> > Mathew coefficient as below: >> > For estimated molecular weight 7919. >> > Nmol/asym Matthews Coeff %solvent P(2.49) P(tot) >> > _____________________________________________________________ >> > 1 26.07 95.29 0.00 0.00 >> > 2 13.04 90.57 0.00 0.00 >> > 3 8.69 85.86 0.00 0.00 >> > 4 6.52 81.14 0.00 0.00 >> > 5 5.21 76.43 0.00 0.00 >> > 6 4.35 71.71 0.00 0.01 >> > 7 3.72 67.00 0.02 0.02 >> > 8 3.26 62.28 0.05 0.05 >> > 9 2.90 57.57 0.11 0.11 >> > 10 2.61 52.85 0.19 0.19 >> > 11 2.37 48.14 0.25 0.25 >> > 12 2.17 43.42 0.22 0.22 >> > 13 2.01 38.71 0.11 0.12 >> > 14 1.86 33.99 0.03 0.03 >> > 15 1.74 29.28 0.00 0.00 >> > 16 1.63 24.56 0.00 0.00 >> > 17 1.53 19.85 0.00 0.00 >> > 18 1.45 15.13 0.00 0.00 >> > 19 1.37 10.42 0.00 0.00 >> > 20 1.30 5.70 0.00 0.00 >> > 21 1.24 0.99 0.00 0.00 >> > _____________________________________________________________ >> > >> > I have at least 10 structures in PDB with homology 60% or above. >> > I tried the CCP4online MrBump and Balbes for automatic molecular >> replacement. No solutions at all. >> > I do not know if this is because that the high number of copies in ASU >> (maybe 10 copies as shown by Mathew coefficient) hamper the MrBump and >> Balbes to do MR? >> > >> > Dose anyone experience similar difficulties with high number of copies >> to do automatic MR? >> > >> > Thanks ahead! >> > >
