The calculations are explained in Appendix A on page 12.
The three estimates of correlation are:
$r_{12}=\frac{s_{12}}{\sqrt{s_{11} s_{22}}}=\frac{0.0056}{\sqrt{0.0309 \times 0.0739}}=0.117189$
$r_{23}=\frac{0.0148}{\sqrt{0.0739 \times 0.0489}}=0.246198$
$r_{13}=\frac{0.0011}{\sqrt{0.0309 \times 0.0489}}=0.028298$
Next we will impose that the common correlation $\bar{r}$ is the average of these 3 values.
$\bar{r}=\frac{1}{3}(0.117189+0.246198+0.028298)=0.130562$
Now I can show you what the matrix F (the constant correlation covariance matrix) looks like. The diagonal entries $f_{ii}$ are taken unchanged from your sample matrix, the off diagonal are found from $f_{ij}=\bar{r}\sqrt{\sigma_{ii} \sigma_{jj}}$
F=[0.0309,0.006239,0.005075;
0.006239,0.0739,0.007849;
0.005075,0.007849,0.0489]
This the shrinkage target.
To find the final result of the Ledoit Wolf approach we have to take a 50/50 compromise (element by element) between your matrix $S$ and the matrix $F$.
$\delta S + (1-\delta) F = 0.5 S + 0.5 F$
(Apologies, I am doing these calculations by hand so there is the possibility of an error).