Let's consider Chang-e 3 as an example, where we'll assume that the lander is our payload and our spacecraft is designed to start in lunar orbit (at 100 km altitude) with enough fuel to make the descent. According to this Spaceflight 101 reference, the specifications are as follows:
- Dry mass of lander: 1200 kg
- Rover: 120 kg
- Wet mass of entire probe: 3780 kg
That wet mass includes the lander, rover, and all the fuel required to transfer from the final launch vehicle trajectory, insert into lunar orbit, and perform the landing. If we consider that to be our spacecraft design, the payload fraction is obviously 3.2%. However, let's do a bit of math and assume that another stage has done the work of inserting us into a lunar orbit -- so how much fuel do we need for descent and landing?
To do this, we'll simplify the problem as being composed of a burn to de-orbit and descend (with apolune at the initial altitude and perilune at the surface), followed by a burn to bring the speed down to null.
In orbit at 100 km (at a radius of 1837.4 km), the speed of the spacecraft is 1.63 km/s from (where $\mu_{Moon} = 4904.9 \frac{km^3}{s^2}$):
$v_{orbit} = \sqrt{\frac{\mu_{Moon}}{r_{Orbit}}}$
Our descent trajectory is an elliptical orbit with semi-major axis $a = 1787.4$ km from:
$a = \frac{1}{2}\left( r_{Orbit} + R_{Moon} \right)$
From that we can compute our speed at the start and end of descent, which gives us $v_{start} = 1.61$ km/s and $v_{end} = 1.70$ km/s:
$v_{start} = \sqrt{\mu_{Moon} \left(\frac{2}{r_{Orbit}} - \frac{1}{a}\right)}$
$v_{end} = \sqrt{\mu_{Moon} \left(\frac{2}{R_{Moon}} - \frac{1}{a}\right)}$
So we'll need an initial $\Delta v$ of about 0.02 km/s to insert into our descent and then a landing $\Delta v$ of about 1.70 km/s to stop the vehicle. That gives a total of 1.72 km/s, and then assuming a specific impulse of $I_{SP} = 300$ s, we can compute our mass fraction. Note we'll assume the final mass is the lander (1200 kg), the rover (120 kg), and some fuel left over that totals 1400 kg.
$\frac{m_{initial}}{m_{final}} = e^{\frac{\Delta v}{g_0 I_{SP}}}$
Substituting those values, we get a mass fraction of about 1.8, and that yields an initial mass of 2520 kg. So for that spacecraft you would have a payload fraction of about 4.8%.