You could just claim your deductible as a Repair Expense on Schedule E. Or, you could depreciate your deductible as an Improvement, as you suggested, though this technically reduces your Cost Basis in the property.
Or, you could claim a Casualty Loss on Form 4684. The FMV before the event would be the amount the insurance reimbursed you, plus your deductible. The FMV after the event is $0. You report the amount the insurance paid you, and in essence you are claiming an Itemized Deduction on Schedule A for your deductible amount.
Here's more info on Reporting a Casualty Loss.
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