Preheat your oven to 325°F (163°C). Line a 9-inch springform pan with parchment paper on the bottom and sides. Allow 10 minutes for the oven to fully preheat.

In a medium bowl, combine 2 cups graham cracker crumbs, 6 tablespoons melted butter, and 3 tablespoons sugar. Stir with a fork until the mixture looks like damp sand with small clumps throughout, about 2 minutes. Checkpoint: The mixture should hold together when squeezed but still have visible crumb texture.

Press the crust mixture firmly into the bottom of your prepared springform pan, using the bottom of a measuring cup to create an even layer. Press from the center outward to avoid gaps. Bake the crust for 8–10 minutes at 325°F until it turns light golden brown and smells toasted. Remove and set aside to cool for 5 minutes while you prepare the filling.

In a large mixing bowl, add 8 ounces softened cream cheese (it should be soft enough to indent with your finger). Using an electric mixer on low speed, beat for 2 minutes until the cream cheese is smooth and creamy, scraping down the bowl halfway through. Do not overmix.

Gradually add 32 ounces cottage cheese (about 3½ cups; drain if very liquid) to the cream cheese, mixing on low speed. Blend for 3–4 minutes, stirring occasionally with a spatula to incorporate stubborn lumps. Small lumps of cottage cheese are acceptable—they add texture—but no large clumps should remain. Checkpoint: The mixture should look creamy and relatively smooth with a slight speckled appearance from cottage cheese.

Add 3 large eggs one at a time, beating on low speed for about 30 seconds after each egg. Stop and scrape the bowl with a spatula between each egg addition to ensure even mixing.

Add 1 cup sour cream, 1/2 cup sugar, 2 tablespoons all-purpose flour, 1 tablespoon cornstarch, 1 teaspoon vanilla extract, 1/4 teaspoon lemon zest, and 1/4 teaspoon salt. Mix on low speed for 1–2 minutes until just combined. Do not overmix; stop as soon as you don't see streaks of unmixed ingredients. Overmixing incorporates excess air and can cause the cheesecake to crack. Checkpoint: The filling should be smooth, pourable, and uniform in color with no visible streaks of unmixed cream cheese.

Pour the filling slowly over the cooled crust, starting from the center and working outward. Fill to about 1/2 inch from the rim of the pan. If using a springform pan, ensure the sides are locked tightly before baking to prevent leaks.

Place the filled pan on a sturdy oven rack positioned in the middle of your 325°F oven. Bake for 50–60 minutes. The cheesecake is done when the edges are set and firm (don't jiggle when you gently shake the pan) but the center 2-inch circle in the middle still jiggles very slightly when you tap the pan. This slight jiggle indicates the residual carryover heat will finish cooking the center without overbaking. Do not wait for the entire top to be firm, or you'll overbake it. Checkpoint: The edges should be opaque and set; the very center should look just barely underdone.

Remove the cheesecake from the oven and allow it to cool undisturbed on the counter for 15 minutes. During this time, the residual heat finishes cooking the center gently, preventing cracks.

In a small bowl, whisk together 2 tablespoons sour cream and 1 tablespoon sugar until the sugar dissolves slightly and you have a pourable, thin mixture, about 1 minute.

Gently spread the sour cream mixture evenly over the warm cheesecake surface in a thin, even layer using an offset spatula or the back of a spoon. Work carefully to avoid disturbing the soft filling beneath. Return the cheesecake to the 325°F oven for exactly 5 minutes. This prevents cracks by creating a protective layer. Remove from oven.

Allow the cheesecake to cool completely at room temperature on a countertop, undisturbed, for 1–2 hours. You'll notice it will continue to set and cool as it sits. Do not move it during this time.

Once fully cooled, carefully run a thin, warm knife around the inside edge of the springform pan to loosen the cheesecake from the sides. Do not remove the pan yet. Place the pan in the refrigerator, uncovered, for at least 6 hours or overnight. Chilling allows the filling to set completely and the flavors to meld.

To serve, remove the cheesecake from the refrigerator 15–20 minutes before serving to allow it to come to cool room temperature (not cold). This enhances the creamy texture and flavor. Wipe a sharp knife with a hot, damp cloth and gently cut the cheesecake into 8–12 slices, wiping the blade between each cut to ensure clean edges. Run the knife around the edge one more time if needed, then carefully open the springform pan latch and lift away the pan sides.