At 5V, the 2N7002 is well suited for this. At 3.3V, borderline -- but it should still work [but I wouldn't trust it for a production design. I'd go with something like the FDV303N -- it's cheap and has a very low Gate Threshold voltage (0.65 to 1V) BUT, it only comes in an SOT23 package, so not hand-solder-friendly. But, if that's an issue, then the 2N7002 is probably just fine.
R1 can be some large value, like 1M, and only acts as a control element before PD3 is configured as a Output [the initial state for an Atmega328 port pin, is Tri-State, which means it will float, and thus the Gate voltage could wind up in a state between "ON" and "OFF", which usually is not desired]. But, because the input impedance of a MOSFET Gate is so high, it doesn't take much to pin it to ground.
Both the FDV303N, and the 2N7002, have a 100nA forward leakage [at TC = 25°C], so 1M*100nA = 0.1V, so no prob since, at 3.3VCC, the VIL threshold is around 1.4V. And, that goes up with higher VCCs. Though, that assumes a Tri-State Hi-Z greater than the impedance of the MOSFET input. I couldn't find a spec for what "Hi-Z" actually means, in the datasheet.
So, the selection of the Gate Pull Down resistor is a trade off between reducing load current on the power source, and making sure the gate doesn't float the MOSFET into it's "active region". If power conservation isn't an issue [for instance, the thing is not being powered by a battery], then use something like a 10k resistor. If, it's battery powered then go higher, like 300k to 1M.