The Federal Deposit Insurance Corporation’s Board of Directors approved Friday the sale of Pasadena-based IndyMac Federal Bank, FSB, to a thrift holding company controlled by IMB Management Holdings LP for a price tag of $13.9 billion. IMB HoldCo is owned by a consortium of private equity investors led by Steven Mnuchin, former Goldman Sachs partner and current co-CEO of Dune Capital Management LP. The complete sale of the bank includes 33 branches, a reverse-mortgage unit and a $176 billion loan-servicing portfolio. The FDIC has agreed to share losses on a portfolio of qualifying loans with New IndyMac assuming the first 20 percent of losses. From there, the FDIC will split losses 80/20 for the next 10 percent of losses and 95/5 thereafter. “The current economic climate is challenging for selling assets, but this agreement achieves the goals that were set out by the Chairman and Board when the FDIC was named conservator of IndyMac in July,” said FDIC Deputy Director James Wigand, the lead negotiator for the transaction. The deal with IMB HoldCo was expected to be announced prior to the first of the year. But the deal apparently hit a snag Tuesday, as sources close to the sale negotiations revealed to HW that Fannie Mae (FNM) was holding the deal hostage and threatening to jeopordize the potential sale. After IndyMac was seized by regulators this summer, Fannie quickly — and quietly — handed the bank a bill for $1 billion, one source said under the condition of anonymity, claiming the failed thrift had violated representations and warranties on various loans sold to the GSE. See full story. HoldCo may very well have used this billion-dollar repurchase claim to push down the sale price.  And even now, Fannie and HoldCo could still be duking it out behind the scenes on what is actually owed for the bad loans. Nonetheless, a final agreement was reached, in which IMB Management Holdings LP and the investor group —  consisting of Dune Capital Management LP, J.C. Flowers & Company, hedge fund firm Paulson & Company, and MSD Capital, LP — will inject a “substantial amount of capital” into the newly formed thrift holding company, according to the FDIC press release. The thrift has also agreed to continue the FDIC’s existing loan modification program –which has been recently championed by FDIC chairman Sheila Bair as golden template for the industry — which has modified 8,512 home mortgages to date, according to Friday’s press release. “The continuation of the loan modification program will be a condition for the FDIC to provide any type of loss-sharing on IndyMac’s assets,” the FDIC stated. The transaction is expected to close in late January or early February. It was determined that the bid from IMB Management Holdings, LP, was the least costly to the Deposit Insurance Fund of all competing bids. It is estimated that the cost to the FDIC’s DIF for resolving IndyMac Bank will be between $8.5 billion and $9.4 billion, in line with previous loss estimates. Write to Kelly Curran at [email protected]. Disclosure: The author held no relevant investment positions when this story was published. Indirect holdings may exist via mutual fund investments. HW reporters and writers follow a strict disclosure policy, the first in the mortgage trade.