The Rafah crossing is the subject of negotiations
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Israel has said the main Rafah border crossing between the Gaza Strip and Egypt will be closed for six months.
Palestinian officials have criticised the closure, implemented on Wednesday, though an alternative crossing out of Gaza will be open at Nitzana.
The move came as Israel's Supreme Court rejected an appeal against demolishing synagogues in Gaza's now abandoned Jewish settlements.
In Gaza, a Palestinian was shot dead and a boy injured by Israeli troops.
The soldiers were guarding an evacuated settlement near Rafah, Palestinian medics said.
The Israeli army said the man had been part of a group trying to cut through the fence of the former Atzmona settlement.
Meanwhile Palestinian militants freed the son of former security chief Moussa Arafat, a mediator in negotiations with the group said.
The Popular Resistance Committees said they had kidnapped Manhal Arafat after shooting dead his father on a raid on their home on Wednesday.
Desecration fear
Israel is due to complete its pullout from Gaza on Thursday 15 September, but defence officials said the operation could be over as soon as Monday.
The Palestinian Authority will take over the Gaza Strip after Israel completes its withdrawal of settlers and soldiers after 38 years of occupation.
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The remnants of trust in the Supreme Court are being destroyed along with the synagogues of Gush Katif
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Correspondents say the Supreme Court ruling on synagogues removes the last obstacle to the Israeli withdrawal from Gaza.
The court accepted government arguments that leaving the buildings intact would leave them open to possible desecration.
The synagogues, which number more than 20, are among the few structures still standing in the abandoned settlements.
A group of leading rabbis had argued that ritual law forbade their destruction.
The Settlers' Council reacted angrily to the decision.
"The remnants of trust in the Supreme Court are being destroyed along with the synagogues of Gush Katif [the main settlement bloc]," a statement by the council said.
Main gateway
Israeli Foreign Minister Silvan Shalom said Palestinian travellers and goods could use the existing Nitzana crossing until Rafah reopened.
"We reached an agreement with Egypt that we will wait six months before we consider opening of the Rafah passages two ways in and out, (while) we get repairs done," he told reporters.
Palestinian Authority officials said the closure of Rafah, which was Gaza's main gateway to the outside world, had not been co-ordinated with them.
They added they would continue to insist on total freedom of movement between Gaza and Egypt, without any Israeli oversight - otherwise, they said, the Israeli occupation of Gaza would not have really ended.
A new terminal now being built by Israel at Kerem Shalom - where the Egyptian, Israeli and Gaza borders converge - would open soon and handle traffic pending a deal with Palestinians on the Rafah urban crossing, he added.
Israel says it wants to preserve a presence on the border, citing doubts about the Palestinian Authority's ability to prevent arms smuggling to militants in Gaza.
International negotiators have been attempting to broker a deal under which Egypt, the Palestinians and a third party would control the Rafah crossing while Israel would monitor it from afar by camera.