A Software City is an established way to visualize metrics such as the test coverage or complexity. As current layouting algorithms are mainly based on the static code structure, dependencies that are orthogonal to this structure often clutter the visualization and are hard to grasp. This paper applies layered graph drawing to layout a Software City in 3D. The proposed layout takes both the dependencies and the static code structure into account. While having the static dependencies encoded in the layout, we can additionally display dynamic dependencies as arcs atop the city in the night view of the Layered Software City. By applying a trace clustering technique we can further reduce the number of shown arcs. We evaluate the advantages of our layout over a classic layouting algorithm in a controlled study on a real-world project and also report on a short study that evaluates the visualization of dynamic dependencies. The source code of the layouting algorithm and the raw data of the quantitative evaluations are available from https://github.com/qaware/holoware-software-city.