Validating Resolution Revolution

Recent advances in instrumentation and image-processing software have resulted in a resolution revolution in cryo-electron microscopy (cryo-EM) and a surge in the popularity of this technique. However, despite technical progress and hundreds of structures determined so far, development of standards assessing the agreement between the cryo-EM map and the respective model has fallen behind. Here we establish a validation procedure evaluating this agreement and applied it to a set of 565 cryo-EM structures. Analysis of the results revealed that three-quarters of the validated structures exhibit moderate or low agreement between the map and the corresponding model, mostly due to limited structural features possessed by these maps. Model re-refinement significantly improved the agreement for only one-fifth of the structures, reaffirming the necessity to re-evaluate map resolution. The presented procedure provides an approach to re-estimate the resolution of cryo-EM map areas interpreted by the model.