The prosecution has alleged the derailment occurred because of a cavalier approach to safety. The defence argued it was unfair to make the five rail executives scapegoats.
The five rail chiefs and Network Rail, formerly Railtrack, deny health and safety charges.
The individual defendants charged are Balfour Beatty Rail Maintenance Limited regional director Anthony Walker, 48, Nicholas Jeffries, 50, civil engineer for the same firm, Railtrack North Eastern managers Alistair Cook, 52, and Sean Fugill, 52, and Railtrack LNE track engineer Keith Lea, 55.
Engineering giant Balfour Beatty admitted earlier that it breached safety standards before the disaster. But the company did not accept all that the prosecution alleged against them.
The company was formally cleared by Mr Justice Mackay of a corporate manslaughter charge. The judge also cleared the five rail bosses of unlawfully killing the four who died.
Mr Justice Mackay told jurors today: 'It has been a long march through this case. We have now come to the end of the part of the case in the court to the vital part that takes place in your jury room.'
He told jurors to take whatever time they needed 'to do justice in this case. Feel no time pressure whatsoever'.
The jury was sent home this afternoon without reaching a verdict. They will continue their deliberations tomorrow.