The recent investigation of an ensemble-based structure calculation using mainly a large collection of exact nuclear Overhauser enhancements (eNOEs) revealed the presence of concerted motion within the protein GB3 (B. Vögeli, S. Kazemi, P. Güntert and R. Riek, Nat. Struct. Mol. Biol., in press). Here, we discuss the method used in this study in detail. Important steps include the NMR pulse sequence, the determination of the eNOEs corrected for spin diffusion, the conversion of eNOE rates into distances, the distance-restraint classification, the use of bundling restraints to generate a compact representation of the structure and the selection of the appropriate ensemble to represent the structure. It is further demonstrated that eNOEs can be obtained between most proton types in a macromolecule. These eNOEs are then used to calculate an ensemble-based structure using CYANA that is capable to reveal long-range concerted motion in the protein. The structure ensembles are cross-validated with jackknife tests applied to the eNOEs, RDCs, scalar couplings, cross-correlated relaxation rates, and with a high-resolution structure obtained independently from X-ray diffraction and refined with RDCs.