Glycoproteins are protein molecules that contain the carbohydrate portion (glycans) covalently attached to polypeptide side-chains, which are assembled in the endoplasmic reticulum (ER) and the Golgi by a controlled sequence of glycosyltransferase and glycosidase processing reactions. The presence of N-glycans controls proper folding of both secretory and membrane-bound proteins. In vitro recombinant glycoproteins are normally badly-glycosylated in the insect or mammalian cell lines, especially the secretory proteins. These N-glycans are usually complex, chemically and conformationally heterogeneous and frequently detrimental to the formation of well-ordered crystal lattices, obstructing the development of protein crystallography. Here we present pattern recognition receptor (PRR) of Arabidopsis FLS2 ectodomain after glycosidases treatment can still heterodimerize with its co-receptor BAK1 induced by flg22 through gel-filtration analysis. Appropriate deglycosylation strategies will not impact the characteristic and native conformation of FLS2 recombinant glycoprotein in vitro assay. The data reveals that Endoglycosidase F (Endo F) but not N-glycosidase F (PNGase F) can reduce the N-glycans of the residues of FLS2 ectodomain in native state, providing the probability of enhancing crystallization or raising diffraction resolution by means of different glycosidase combination and optimization.