No, the square feet is what is used to determine the deductions based on that space amount. Any business equipment or property in the space that is used 100% for business will help, however the space itself is captured by the square feet of the office space, divided by the square feet of the entire home to arrive at the business use percentage of the home expenses to determine the allowable expenses strictly related to the home overall (utilities, insurance, taxes, mortgage interest).
The cost of the home, less land, will be determined by the same percentage for your depreciation.