A method is described for merging in reciprocal space of electron microscopic data from three-dimensional crystals of the acrosomal bundle. Permutation of indices was required to find the proper alignment of data from different bundles. The method utilizes a statistical evaluation of the significance of the cross-correlation results to indicate the proper order for merging. The three-dimensional (313) merging is a reference-free operation that does not depend on choosing a "zero-tilt" user-defined starting point. Results from the merging are given and the merged 3D data to 9.5 Angstrom resolution is evaluated for coherence. General issues such as statistical significance of cross-correlation function peaks, symmetry evaluation, and phase coherence as a function of amplitude are discussed. (C) 2003 Elsevier Inc. All rights reserved.