These 27 tilt series were collected from two different types of control samples using a FEI Tecnai F30 electron microscope and were control data of EMPIAR-10157. A sub-tomogram average derived from the first 20 tilt series (S1-S20) of EHNA inhibited immotile sea urchin sperm flagella has been deposited in EMDB under ID code EMD-8835; A sub-tomogram average derived from the last 7 tilt series (S21-S27) of the other control sample (Triton X-100 demembranated sea urchin flagella) has been deposited in EMDB under ID code EMD-8837.