The question asks which experimental discovery contradicted Thomson's model of the atom. Let's explore the options and find out the correct one by understanding what each discovery involved and how it relates to Thomson's model:

1. Alpha particle scattering showing deflection at large angles: This is the correct answer. Thomson's model, also known as the "Plum Pudding Model," depicted the atom as a sphere of positive charge with electrons embedded within it, like plums in a pudding. According to this model, the positive charge should be spread out so that alpha particles passing through an atom should not be deflected significantly. However, Rutherford's gold foil experiment showed that some alpha particles were deflected at very large angles, which could only be explained if the atom had a small, dense, positively charged nucleus. This discovery directly contradicted Thomson's model and eventually led to the development of the Rutherford model of the atom.
2. Measurement of atomic radius using X-ray diffraction: This measurement concerns the determination of atomic size but does not directly address the distribution of atomic charge or the structure of the atom that could refute Thomson's model.
3. Discovery of the neutron by James Chadwick: The discovery of the neutron in 1932 added to our understanding of atomic structure, explaining the extra mass in the atomic nucleus, but it did not contradict the charge distribution as suggested by Thomson's model.
4. Observation of line spectra of hydrogen by Bohr: Bohr's work on the hydrogen line spectra addressed atomic electron energy levels and led to the Bohr model. While it further developed the understanding of atomic structure, it was not this observation that directly contradicted Thomson's model.

Based on this analysis, the discovery that contradicted Thomson's model of the atom was Alpha particle scattering showing deflection at large angles.