Thanks for all of the helpful suggestions. In reply to some of the comments, I did purify by eluting with imidazole from a Ni-NTA column. The imidazole I used is 99% pure, although I'm not sure whether it is reagent or molecular biology grade. I also do use DTT in my lysis and elution buffers, so these could contribute to the color.
After Ni-NTA, I dialyzed the protein into a buffer containing 10 mM Tris, pH. 7.0, 10% Glycerol, as BME overnight, and then purified it on a Q-column. I then did a final dialysis in buffer that contained 2 mM DTT and 5 mM MgCl2 (although the color appears without the MgCl2 as well), among other reagents. I would think that the two dialysis steps and the Q-column would remove all of the imidazole. However, I did not run the protein on a sizing column or use EDTA in any buffers. I could try using a sizing column, and if that does not remove the color, I could use some of the techniques suggested to determine if any metals are bound. Matt
