Johannes Mehserle, the BART cop who shot and killed an unarmed man in Oakland on New Year’s Day, sat behind bars in a Bay Area jail on Wednesday night, charged with murder.

Appearing in a Nevada court Wednesday, Mehserle waived extradition and returned to the Bay Area, where he was taken to Santa Rita Jail on the murder charge — a rare filing against a police officer — that was announced by Alameda County District Attorney Tom Orloff.

Mehserle’s arrest, however, for the shooting of 22-year-old Oscar Grant III, did little to dampen the outrage in a city already beleaguered with economic troubles and skyrocketing crime.

Ever since Grant’s shooting was captured on a cell phone and widely replayed on national television and the Internet, protests have erupted in San Francisco and Oakland, where many residents have had long-running tension with law enforcement.

Wednesday evening, protesters once again took to the streets, in a largely peaceful rally of more than 1,000 that began with a march in downtown Oakland amid a heavy police presence. At first, the protest appeared to be in sharp contrast to the violent demonstration last week that led to the vandalism of dozens of buildings and the arrest of more than 100 people in the city’s downtown business district. But as the night wore on, a splintered group of demonstrators began a rampage through downtown, smashing windows at a dozen businesses, vandalizing several cars and forcing police in riot gear to spray tear gas. At least 18 people were arrested, the majority on suspicion of felony vandalism.

Witnesses told authorities that Mehserle fired a shot into Grant’s back while Grant was lying facedown on a train platform at the Fruitvale BART station in Oakland. Grant and others had been pulled off a train after reports of fighting, as New Year’s Eve revelers headed home after midnight.

New court documents say Grant had his hands behind his back and another officer was kneeling on his neck when he was shot.

The allegations were revealed in an Oakland police officer’s request for an arrest warrant. It said it appeared from cell phone video that “Mehserle shot and killed Oscar Grant while Grant was restrained and unarmed.”

Mehserle surrendered without incident Tuesday at a family friend’s house in an upscale neighborhood on the east shore of Lake Tahoe in Douglas County, Nev. His lawyer said his client had gone there to escape death threats and to get away from the pressures of the case, not to avoid arrest.

Mehserle, 27, who resigned after the shooting, is expected to be arraigned today in Oakland.

“As this case moves forward through the justice system and all of the circumstances of that chaotic night become clear, I fully expect Mr. Mehserle will be cleared of the charges against him,” said his lawyer, Christopher Miller. ﻿”The case won’t be tried by video alone. I’m confident that this case is not just about a video. It’s not just about certain circumstances that folks may want to focus on.”

Orloff said he would not speculate on whether the charge would end up being first-degree murder or second-degree murder, saying the complaint “doesn’t specify the degree, it merely charges murder.”

“At this point, what I feel the evidence indicates, is an unlawful killing done by an intentional act, and from the evidence we have there’s nothing that would mitigate that to something lower than a murder,” Orloff said at a news conference.

First degree murder is a premeditated, intentional killing that carries a sentence of 25 years to life. Second-degree is an intentional killing that is not premeditated or planned and carries 15 years to life.

John Burris, the attorney for Grant’s family, which has filed a $25 million claim against BART, expressed satisfaction over the new charges.

“It is consistent with the evidence I have seen. I think the family will be pleased,” Burris said.

Meanwhile, the Napa Valley Register reported that Mehserle’s family in Napa received a bomb scare. Residents in their southeast Napa neighborhood were evacuated after Mehserle’s parents found two unidentified packages late Wednesday on their front porch.

Mehserle has refused to be interviewed by either BART investigators or Orloff.

At Wednesday’s protest, Grant’s grandfather, also named Oscar Grant, stood in the middle of the street and said, “We got to stop these people who have a gun and a badge and a license to kill.”

The Associated Press contributed to this report.