Atomic defects are controllably introduced in suspended single layer molybdenum disulfide (1L MoS2) using helium ion beam. Vacancies exhibit one missing atom of molybdenum and a few atoms of sulfur. Quantification was done using a Scanning Transmission Electron Microscope (STEM) with an annular detector. Experimentally accessible inter-defect distance was employed to measure the degree of crystallinity in 1L MoS2. Correlation between the appearance of an acoustic phonon mode in the Raman spectra and the inter-defect distance was established, which introduces a new methodology for quantifying defects in 2D materials.