I say Find a legendary that stays in one spot (Kyogre, Groudon, Rayquaza Lati@s on Southern Island, a Regi, Lugi/Ho-oh, Deoxys, or Mew, Preferably one of the three weather trio pokes, or the Lati@s.) Then stand in front of it and save your game. Catch it with the Masterball and find out if it has a good nature and IVs, or is a shiny. If it isn't, simply soft-reset and try again. (I caught 2 Kyogre both with perfect special attack and a modest nature, A modest Mewtwo, and a perfect special attack bold Latias this way.) That way you are sure to get your masterball's worth, however like others are saying it would be better for you to clone it after beating the E4.