Dear Pankaj Kumar,

The main problem is not to guess what and how to fit but rather how to go about the process of finding out what it is. Unless you find an automated tool for electron density fitting and identification you have to create a process that would in the end provide the best choice.

1) Refine the best you can everything else. That includes all small and large conformational errors of your protein/any other macromolecule you refine.

2) Refine all the elements of the solvent that are easily identifiable. This contains metal ions, water molecules, glycerol, and the easily identifiable buffer components (Tris, Hepes, Cacodylate, phoshates etc.etc).

3) Try to fit any of the already identified molecules to this density and refine it. Learn how to judge the fit by analyzing difference electron densities: negative/red map too much electrons, positive/green map not enough.

4) Learn how to use the information that is provided by high fidelity ED map.

This includes measuring the number of electrons at the particular site by sliding the cutoff of the contouring level of you 2Fo-Fc map. For instance phosphates are much more electron dense objects than carbon centers, metal ions are much more electron dense centers than phosphates etc. You can easily learn that by changing the conturing level dynamically. Actually at the resolution ~1Å you can actually measure a contribution of individual electrons and differentiate nitrogen, from carbon, from oxygen atoms.

But be honest the simplest is to do some biochemical/chemical analytic work.

If desperate try to understand the general shape of the object. i.e. branching structure. Your density is reminiscent of a fragment of a phospholipid with a phosphate center and some lower electron density legs. Unfortunately, the occupancy would always mess up this type of analysis and the FAD with something attached can produce such shapes at lower occupancy levels.

Good Luck.

Bog

Dear Pankaj,

Based on the figure you provided I would suggest to use EDO (ethylene glycol)

the right portion of your PEG.

The positive density looks heavier than oxygen (water).

Check if you had any metals in solution, should be heavier than Na (sodium) or Mg (magnesium).

I would think it could be Ca (calcium) or some heavier metal.

Peaks surrounding it could be water molecules. Maybe you have partially hydrated metal ion.

Best.

George.

Thank you Boguslaw Stec