Atomic structure analysis of crystalline materials is a paramount endeavor in both chemical and material sciences. This sophisticated technique necessitates not only a solid foundation in crystallography but also a profound comprehension of the intricacies of the accompanying software, posing a significant challenge in meeting the rigorous daily demands. For the first time, we confront this challenge head-on by harnessing the power of deep learning for fully automated routine structure analysis at the full-atom level. To validate the performance of the model, named CrystalX, we employed a dataset comprising over 50,000 X-ray diffraction measurements derived from authentic experiments. Under a strict temporal validation scheme that separates training and test data by publication time, CrystalX substantially outperformed the automated baseline and adept at deciphering intricate geometric patterns. Remarkably, CrystalX revealed that even peer-reviewed publications harbor expert interpretation errors that can evade stringent CheckCIF A/B-level alerts, yet CrystalX adeptly rectifies them. It has already been successfully applied in our day-to-day pipeline, enabling fully automated, human-free structure analysis for newly discovered compounds. Overall, CrystalX marks the beginning of a new era in automating routine structural analysis within self-driving laboratories.