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What makes San Francisco so great on defense is a combination of a bend-don't-break mentality, instilled by coaches Mike Singletary and Greg Manusky, and the players they put on the field.
Patrick Willis is the best linebacker in the game, and probably the most physically gifted one too. Anyone who saw his pregame chat with Jon Gruden was quickly alerted to how hard Willis studies tape and prepares for games.
Lining up around the game's best linebacker is a very good defensive corps. Takeo Spikes plays the other inside linebacker in the 3-4. He's not as young and spry as he once was (a knee contusion during the Monday night game doesn't help), but he still manages to raise a ruckus against offenses. Justin Smith makes a ton of tackles from defensive end. Nate Clements has made a career out of being a solid cover corner who is excellent playing the run.
But the defense's anchor is Aubrayo Franklin. Like Pittsburgh's Casey Hampton, he's a shorter defensive lineman, but that's what makes him perfectly suited to play nose tackle. At 6'1'' and 317 pounds, it takes a lot to get under his pads and get him moving anywhere but where he wants to go.
Franklin was a hold out this training camp. To know exactly how much he's worth to the 49ers, just look at what they paid to get him playing again—$7 million. That's a lot to pay for a lineman who's 30, and by paying it the 49ers are showing he's worth it.
Against the pass, San Francisco is slightly worse off. It doesn't make them terrible, they're just not as good as they are against the run. In Week 1 at Seattle, the Seahawks rushed for just 13 yards in the first half, and still led by eight via a combination of passes, play action, and turnovers. They'd still finish the game averaging just 3.3 yards a rush though.
The first Seattle touchdown came on a play-action pass, which turned into Matt Hasselbeck sprinting for the corner pylon. He got there and put the Seahawks up 7-6. It would be all they needed to win the game, but it was just part of what New Orleans needed.