Step 1Heat the oven to 350 degrees. Lightly butter a 9-inch springform pan and set it aside
Step 2Finely chop the pecans with 3 tablespoons of the sugar in a food processor. Transfer the mixture to a medium bowl. Process the graham crackers in the food processor to fine crumbs. Measure 1 1/4 cups crumbs, add them to the bowl of pecans and mix well. Add the melted butter and mix well.
Step 3Press the crumb mixture in an even layer on the bottom and about 1 inch up the sides of the pan. Bake for 10 minutes. Let cool completely.
Step 4Leave the oven at 350 degrees.
Step 5Beat the cream cheese with 1/2 cup sour cream at low speed in the bowl of an electric mixer until very smooth, scraping down the sides of the bowl once or twice with a rubber spatula. Gradually beat in 3/4 cup of sugar. Beat in the eggs, one by one. Stir in the lemon and orange zests, lemon juice and 1 teaspoon of vanilla. Carefully pour the filling into the cooled crust.
Step 6Bake the cheesecake until the center is just firm, 45 minutes. Remove the cake from the oven and cool for 15 minutes. Increase the oven temperature to 425 degrees.
Step 7Mix together the remaining 1 1/2 cups sour cream, 3 tablespoons sugar and 1 teaspoon vanilla in a small bowl. Carefully spread the topping on the cake, in an even layer, without letting it drip over the crust. Bake the cake 7 minutes to set the topping; it will still look soft but will become firmer as it cools. Remove the cake from the oven and cool it to room temperature.
Step 8Refrigerate it at least 2 hours before serving. Just before serving, remove the sides of the pan and garnish the cake with the berries.