RNA Polymerase II (Pol II) is the central enzyme in eukaryotic mRNA transcription. In recent years, structural studies have provided insights into the mechanism of Pol II. A full understanding of the mechanisms of transcription will require structural insights into the numerous complexes of Pol II with transcription factors involved in in vivo transcription. However, these structural studies are hampered by the limited resolution produced by crystals of such complexes. Improved crystallographic methods designed to enhance structural data obtainable from such complexes have been developed taking advantage of the anomalous scattering due to intrinsic zinc ions in Pol II. These approaches have been validated using the known structure of 12 subunit Pol II, and were able to provide additional insights into its structure.