Jn 19:31-33  Since it was the day of Preparation, and so that the bodies would not remain on the cross on the Sabbath (for that Sabbath was a high day), the Jews asked Pilate that their legs might be broken and that they might be taken away. 32 So the soldiers came and broke the legs of the first, and of the other who had been crucified with him. 33 But when they came to Jesus and saw that he was already dead, they did not break his legs. (ESV)

Jn 20:25  So the other disciples told him, “We have seen the Lord.” But he said to them, “Unless I see in his hands the mark of the nails, and place my finger into the mark of the nails, and place my hand into his side, I will never believe.”

Some scholars used to think the crucifixion story was contrived because it was thought that the Romans used ropes, not nails, to secure victims of crucifixion to the cross.  It was also thought that such victims were only thrown in common graves, not given proper burials.  But in 1968 Vassilios Tzaferis found an ossuary containing the bones of Yohanan Ben Ha’galgol in northern Jerusalem.  It was contained in a tomb with ~35 other bodies.  Yohanan was killed by crucifixion sometime between AD 7-70.  He still had a 7” nail in his right heel and his legs were broken (as described in Jn 19:32-33).  Apparently the nail in his right heel had hit a knot in the wood of the cross and could not be removed from the ankle when attempting to remove Yohanan from the cross.  To get him off the cross they had to remove part of the cross itself, leaving the nail in his heel.

Traces of olive wood were found between the head of the nail and the bone, indicating that there was a piece of olive wood placed over the man’s foot before the nail was driven in, probably to make it more difficult for the man to free his legs.  Unlike Jesus, this man’s feet were nailed to the side of the cross individually.  It’s also possible that his arms were tied to the cross by ropes rather than nails, with some sources claiming there is evidence of nails in his wrists while others claim there is not.

As for giving crucified victims a proper burial, in addition to the discovery of Yohanan's crucified body, we also have the testimony of Josephus that this was a common Jewish practice: 

Nay, they proceeded to that degree of impiety, as to cast away their bodies without burial, although the Jews used to take so much care of the burial of men, that they took down those that were condemned and crucified, and buried them before the going down of the sun. (Jewish War 4.5.2).

Significance:
  1. This confirms that some victims were nailed to the cross.
  2. This confirms that victims of crucifixion could be granted a proper burial as Mk 15:42-47 indicates.
  3. This confirms that victims of crucifixion would routinely have their legs broken to hasten death.