The 3D structure of a protein/ligand (PDB format) can be extracted from XRD data using crystallographic software such as Olex2. Olex2 is an open source software that allows you to analyze and manipulate XRD datasets. With Olex2, you can generate 3D models from your XRD data by refining the crystal structure and determining the parameters needed for the model. This process is called "structure determination". Once you have the parameters, it is then possible to generate a PDB format file.