Uninsured deposits at IndyMac Bancorp totaled about $541 million, federal regulators said Thursday, marking their second reduction of the estimate since the government seized the troubled mortgage lender July 11.

The Federal Deposit Insurance Corp., which is operating the Pasadena savings and loan and is hoping to sell it, originally estimated that $1 billion of IndyMac’s $19 billion in deposits were uninsured. Last month, the FDIC revised the figure down to about $600 million.

The latest change resulted from the slow process of interviewing depositors about complicated accounts, especially trust accounts for which every beneficiary must be verified, FDIC spokesman David Barr said. Basic FDIC insurance tops out at $100,000 per customer at a bank, thrift or credit union, but depositors can insure many times that amount by setting up joint accounts and trusts.

The FDIC now estimates that IndyMac’s collapse will cost the federal deposit insurance fund $8.9 billion.