Low affinity protein complexes are difficult to isolate and handle in crystallization experiments. Size-exclusion chromatography often does not allow purification of the homogeneous complex. Here we used a size-filtration approach for the purification and concentration of the 19 mu M affinity complex of yeast Rab-GTPase and its guanine nucleotide disassociation inhibitor (GDI). The homogeneous protein complex solution was crystallized and the structure was solved using the molecular replacement method. The resulting model of the low affinity unprenylated Rab-GDI complex should reflect a transient Rab-GDI complex when GDI is bound to the membrane-anchored Rab protein and is poised to extract Rab to cytosol. (c) 2007 Elsevier Inc. All rights reserved.