Are the amounts in Box 1, 3, and 5 usually the same value? Should Box 3 and 5 only show a percent of the amount in Box 1?

It is very common for all three to be same.  Things that can cause them to be different are retirement plan deductions 401(k) or 457 plan, someone whose income is above the social security income threshold.  If you aren't contributing pre-tax to a retirement plan, and your income is $50,000, it would be normal.