Dear Rongjin, In addition to all suggestions, you would also want to check 2007 proceedings of CCP4 study weekends about crystallography of complexes.
http://www.ccp4.ac.uk/ccp4course.php I also liked following papers that give you so much information about crystallization of protein-ligand complexes. 1. Crystallization of protein-ligand complexes. PMID : 17164529 2. The use of biophysical methods increases success in obtaining liganded crystal structures. PMCID: PMC2483471 Sincerely Amit Gandhi
