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In the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin–spin distances at nanometre-scale by measuring dipole–dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO.

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Pulsed dipolar electron paramagnetic resonance (PDEPR) spectroscopy experiments measure the dipolar coupling, and therefore nanometer-scale distances and distance distributions, between paramagnetic centers. Of the family of PDEPR experiments, the most commonly used pulsed sequence is four-pulse double electron resonance (DEER, also known as PELDOR). There are several ways to analyze DEER data to extract distance distributions, and this may appear overwhelming at first. This work compares and reviews six of the packages, and a brief getting started guide for each is provided.