Married joint filing, each qualified for $5000 tax treaty(resident alien on F1, PRC citizen). However, my wife has income less than $5000. Can we deduct combined $10000?

If she has $1000 dollar income, can I deduct that $1000? or can I still enter $5000 for her?

I noticed that even if I just deduct $1000, we are getting more back than the tax withheld from her W2… Is this fine?

More details: she is actually non-resident alien. But I am resident alien, passing substantial presence test. We are jointly filing and treating her as resident alien.