[phenixbb] refinement of ligands and waters

Alexandra Marques at.marques at fct.unl.pt
Wed Jun 10 04:48:07 PDT 2015


I still have little experience in the refinement of protein structures. So,
I have some (basic) doubts that I would like you to help me please.

1) I have a metal coordinated to a cofactor in the active center of my
protein structure. The initial solution provided by phaser/autobuilding
already contained the metal+cofactor modelled in the density but with zero
occupancy. Then I created all the necessary restraints and cif files with
phenix_ready_set and did two cycles of model building/phenix refinement.
The refined structures always contained zero occupancy for those atoms. My
question is: should I manually change the occupancy for the metal+cofactor
to 1? I thought this would be made automatically by phenix because I
selected the option “occupancies” and “individual B-factors” in the
refinement strategy…

2) When manually placing waters in the density with coot, what is the
maximum value of B-factor that is acceptable for a water? I am asking that
because I have some water molecules with weak density and consequently
B-factors between 45 and 55 but that are involved in interactions with
other molecules. Is it better to keep those waters or remove them?

Best regards,

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