Single crystals of the Kitaev spin-liquid candidate $alpha$-RuCl$_3$ have been studied to determine low-temperature bulk properties, structure and the magnetic ground state. Refinements of x-ray diffraction data show that the low temperature crystal structure is described by space group $C2/m$ with a nearly-perfect honeycomb lattice exhibiting less than 0.2 % in-plane distortion. The as-grown single crystals exhibit only one sharp magnetic transition at $T_{N}$ = 7~K. The magnetic order below this temperature exhibits a propagation vector of $k$ = (0, 1, 1/3), which coincides with a 3-layer stacking of the $C2/m$ unit cells. Magnetic transitions at higher temperatures up to 14~K can be introduced by deformations of the crystal that result in regions in the crystal with a 2-layer stacking sequence. The best fit symmetry allowed magnetic structure of the as-grown crystals shows that the spins lie in the $ac$-plane, with a zigzag configuration in each honeycomb layer. The three layer repeat out-of-plane structure can be refined as a 120$^o$ spiral order or a collinear structure with spin direction 35$^o$ away from the $a$-axis. The collinear spin configuration yields a slightly better fit and also is physically preferred. The average ordered moment in either structure is less than 0.45(5) $mu_B$ per Ru$^{3+}$ ion.
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