Structural genomics initiatives select targets that are likely to express as soluble stable species in recombinant systems.  Even with this inherent bias towards soluble single proteins, statistics (from the PSI structural genomics centers, for example) indicate that only 67% of the selected targets can be expressed, less than 25% of those ever produce soluble protein, and less than 3% result in a crystal structure.  In order to advance methodologies for the increased structural coverage of proteomes, we investigated the feasibility of using protein isolation from native sources as a protein pipeline for crystallization studies.  Using large scale fermentation, protein production was scaled up and, using microfluidic technology, crystallization was scaled down. This allowed us to delve into the native proteome of the model organism E. coli using a “macro-to-micro” approach.  From one kilogram of cells, we were able to successfully crystallize 28 proteins, 4 of which were novel.  The general utility of this approach is not limited to bacteria, but can be easily adapted to study the proteomes of higher organisms.  These results validate the “macro-to-micro” whole proteome approach as a complementary method to traditional structural genomics initiatives, feasible in a single laboratory, for accessing native proteomes for structural characterization.