Which DVD are you following? Most of those I've seen feature electric guitars which produce a totaly different sound to a good old Fender acoustic.
So, your guitar is in tune, and as the E5 power chord uses the open 6th string your whole problem is tied up between the two fretted notes on the 4th and 5th strings.
Drop the 4th string note for the moment and play the E5 chord using just the open 6th string and the fretted 5th string. You don't lose anything playing power chords this way as the 4th string just doubles the root note on the 6th string an octave higher.
Use your fretting hand ring finger on the second fret of the 5th string (when you come to play higher position power chords you'll realise that using the ring finger is the only way to make the stretches). Make sure your finger is close to but behind the fretwire and give it some welly. There's something like 60 pounds of tension in a steel guitar string which is sufficient to support a very large fish, so you're pushing down against a lot of tension.
Make sure the finger holds the string down firmly and play just the 5th string. We'll assume you get a decent sound. If not, re-do the exercise using the middle finger of your fretting hand.
Now make sure you can play the open 6th string without the fretting hand finger impeding its movement. We'll assume you get a nice clear sound out of the 6th string.
That should be enough to get a good sound for the E5 power chord, but remember that acoustic guitars and power chords are not really made for each other.
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