Thank you for your question.
This is relevant to your scenario ....
Married couples & civil partnerships
For the purpose of property ownership, married couples and civil partnerships are seen as one unit. This means that if one person already owns a property, any subsequent residential purchase by either person will be seen as an additional property for both individuals.
Married couples living separately, who are separated in circumstances that are likely to be permanent, will now be treated individually and not as one unit.
Stamp Duty does not apply to inherited property so there is no SDLT to pay. If someone who has inherited a property then goes on to purchase another home this could be counted as an additional property.
If however someone has inherited a small share (50% or less) in a single property within 36 months prior to purchasing a new property, they should not be liable for the higher SDLT rate.
This exemption has been introduced to provide flexibility for purchasers who may find it difficult to dispose of a share in an inherited property.
You say your wife inherited 25% of a property about 4 years ago (more than 36 months prior to purchasing a new property).
More information on this can be found here
Having considered both aforementioned points, it appears you would be liable to additional 3% stamp duty. I am sorry if this is not what you expected.
I hope this is helpful and answers your question.
If you have any other questions, please ask me before you rate my service – I’ll be happy to respond.