[phenixbb] most appropriate map for ligand fitting/interaction withFMN

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Sun Mar 13 01:57:31 PST 2011


a)I second Pavel's comments. Usually I look at 2fofc and fofc maps after
2 rounds of refinement. In the first round automated water placement
takes place, before the second round I'll delete a sphere of water from
the active site to get an unbiased and less cluttered view. The
underlying rationale is to 'squeeze' as much as possible out of the
maps/phases before placing a ligand. Some other people prefer maps after
refinement w/o waterplacement. As mentioned kicked maps are a great tool
to get you over the hump in case of some ambiguous cases, I use them on
a routine basis.

b) Tough to say w/o looking at the maps and molecules. Some things come
to mind:
   - how does the QC of your ligand look, is it pure?
   - how does your apo protein or the protein with the FMN compare to
the liganded structure?
   - counter ions in crystallization/purification/storage buffers?



> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Yuri
> Sent: Sunday, March 13, 2011 5:38 AM
> To: phenix forum
> Subject: [phenixbb] most appropriate map for ligand
> withFMN
> I am refinig a structure at 2.1 A. I have 2 questions:
> a) Is the best way to identify a ligand refining the protein and water
> molecules and at the end looking at the 2mfo-dfc and mfo-dfc maps? Or
> looking at a SA composit omit map?
> b) In almost every map i look at during refinement I see density that
> smears/joins my ligand (cyclopentenone type molecule) and flavin's
> isoalloxazine ring. Has anyone ever seen that? they seem to be 3.1 A
> apart?
> Thanks
> --
> Yuri Pompeu
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