Hello,
Have diffraction data about a protein that has the "79.06 79.06 79.50 90.00 90.00 120.00" unit cell. When using the model structure as a dimer or hexamer, I couldn't take any results, taking continuous error for both in Phenix terminal and Phenix GUI. Also, although I entered the monomer model structure on the Phenix (terminal or GUI), I always took two dimer structures (MR.1.pdb) (Figure-2, up). Im completely confused at that point.
Normally, in PDB, this protein is a dimer form (XRD result), and we can generate its symmetry that has a single hexamer form (Figure-1). But I took two dimers from MR result, so when i generate its symmetry, it gives two separate hexamer forms of the relevant structure (Figure-2).
When I use the terminal for molecular replacement, I obtained a result that has Rwork: 0.56 value. When i use the GUI for molecular replacement, this time i took a result that has Rwork: 0.28 value (that looks perfect!). But as i said before, the structure pdb that is given by molecular replacement is a dimer, unlike the monomer that i entered as a model structure.
Can't understand what the problem is,
is it the problem (?): during the refinement process, there is an element of symmetry that was overlooked in my refined model in the P3 space group? In fact, my single-molecule layer supports P6 symmetry, which originates in the center of a hexamer. When I make my initial space group P3 for the crystal, my unit cell cannot be double in the "c" axis, a shift occurs between the molecular layers. Although there was originally hexameric symmetry diffraction, we can't see it coherently in the model structure (Figure-3)?
Would be incredibly happy if you could help me with this. Need an urgent solution
Thank you in advance
Kind regards,
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