Most of these waters are of no significance to the function of the protein, and they probably do not reside in the same positions in solution. But adding models of the water molecules revealed by the map makes the overall model more complete and accurate, and thus improves the accuracy of calculated phases and the clarity of the map. The resulting model is as accurate as the data allows. The atomic coordinates of this model are then deposited in the Protein Data Bank. In addition to the coordinates, the PDB file contains some other useful information.
Smaller R is better.
For proteins, a desirable target R-factor for a model at 2.5 angstrom resolution is 0.2. The R-factor for a model in early stages of structure work may be as high as 0.4, but with each successive rebuilding stage, R should decrease. Crystallographers use the R-factor to show them how well the procedure is going. A good model should show average devations from expected values of no more than 0.2 angstroms in bond lengths and 4 degrees in bond angles. Another result of crystallographic structure determination is a number called a B-factor or temperature factor for each atom.