Laser pulses in current ultra-short TW systems are far from being ideal Gaussian beams. The influence of the presence of non-Gaussian features of the laser pulse is investigated here from experiments and 3D Particle-in-Cell simulations. Both the experimental intensity distribution and wavefront are used as input in the simulations. It is shown that a quantitative agreement between experimental data and simulations requires to use realistic pulse features. Moreover, some trends found in the experiments, such as the growing of the X-ray signal with the plasma length, can only be retrieved in simulations with realistic pulses. The performances on the electron acceleration and the synchrotron X-ray emission are strongly degraded by these non-Gaussian features, even keeping constant the total laser energy. A drop on the X-ray photon number by one order of magnitude was found. This clearly put forward the limitation of using a Gaussian beam in the simulations.