[phenixbb] metal refinement: adps and restraints

Alexandra Marques at.marques at fct.unl.pt
Thu Jul 2 09:14:19 PDT 2015


I am refining a protein with a Mo in the active site and which is bound to
a cofactor and to a water molecule. After each refinement step there is
always a lot of positive and negative density around the Mo and the
cofactor molecules, although their occupancy refined to 1. I read this
message http://www.phenix-online.org/pipermail/phenixbb/2015-May/022031.html,
but I still have doubts about how to choose the refinement parameters. I
know I have to select the Mo atoms to be refined anisotropically. And the
other atoms, do I have to specifically select them to be refined
isotropically?. For instance:

Isotropic atoms: not element Mo

Anisotropic atoms: element Mo

I am asking that because I have been using TLS for the protein atoms during
refinement, so I am not sure if it is correct to select the other atoms as
isotropic or if I leave it in blank…

My other problem is with the metal restraints. I am not sure about the
ideal distance between the Mo and O atom but based on homologous protein
structures I choose the following:

 refinement.geometry_restraints.edits {

  bond {

    action = *add

    atom_selection_1 = name MO   and chain A and resname 4MO and resseq 1

    atom_selection_2 = name  O   and chain A and resname O and resseq 2

    distance_ideal = 1.900000

    sigma = 0.050



However after the refinement this ideal distance interval (1.95-1.85) is
not respected; I have 4 active sites and in some of them the Mo-O distance
refines to 0.83 A although there is a lot of density for the water molecule
to be at 1.9 A. How to make the restrainst work? Am I missing something?

Thank you very much,

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