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[ccp4bb]: Refinement of ligand occupancy



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I am a graduate student working on my first structure determination of a
heme protein (HOPEFULLY) bound to a ligand.  The assumption is that the
ligand will displace AN axially bound water molecule.  I have run into a
problem with trying to refine the occupancy of the ligand.  I have already
attempted to use CNS to refine the occupancy of the ligand.  I have used
both the q-group and q-individual and harmonically restrained (with various
intensities) all or part of the ligand.  I generated another Fo-Fc electron
density map after the>refinement step and did not see any improvement.  I
have a few questions and any opinions would be helpful.

1)  Are there other routines that are recommended for refining occupancy of
a ligand?  For example should the whole ligand be restrained or constrained
at the beginning of refinement and then the restraints or constraints lifted
later in refinement and allow the ligand to refine freely?

2)  What kind of positive and negative indications should I be paying
attention to - for example should values of refined occupancy or B-factors
change SUBSTANTIALLY?  What indication would I see if the ligand is PRESENT
But at low occupancy?  Should I expect to see any changes in the R-factor or
Rfree values after only 1 cycle of refinement?



------------------------------------------------------------
Daniel M. Copeland 
Graduate Student (Biochemistry/Inorganic Division)
Department of Chemistry and Biochemistry
University of Oklahoma              Lab Tel: 405-325-1532
620 Parrington Oval                 FAX: 405-325-6111
Norman, OK  73019                   email: dcopeland@ou.edu