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Manipulating defence responses in infected host cells is a prerequisite for filamentous plant pathogens to complete their life cycle on infected host plants. During infection of its host Arabidopsis thaliana, the oomycete pathogen Hyaloperonospora arabidopsidis secretes numerous RXLR-type effector proteins, some of which are translocated into host cells. RXLR-type effectors share conserved N-terminal translocation motifs but show high diversity in their C-terminal `effector domains' that manipulate host defence mechanisms. Therefore, obtaining structural information on the effector domains of RXLR-type effectors will contribute to elucidating their molecular-virulence functions in infected host cells. Here, the expression, purification and crystallization of the effector domain of RXLR3 from H. arabidopsidis isolate Waco9 are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 61.49, b = 27.99, c = 37.59 Å. X-ray data were collected to a resolution of 1.8 Å from a single crystal using synchrotron radiation.