most appropriate map for ligand fitting/interaction with FMN
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
Hi Yuri,
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?
These are good to look at. This is why phenix.refine outputs them. Ligand-omit kick map may be a quick way of getting less model biased residual omit map for your ligand.
Or looking at a SA composit omit map?
This may may be useful if you want to prove something or in doubt.
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?
I'm not quite sure what you mean - it's hard to discuss a map without looking at it.. Pavel.
Yuri, 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? HTH Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Yuri Sent: Sunday, March 13, 2011 5:38 AM To: phenix forum Subject: [phenixbb] most appropriate map for ligand fitting/interaction 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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participants (3)
-
Pavel Afonine -
Schubert, Carsten [PRDUS] -
Yuri