In my experience, good quality, well-refined protein structures have a resolution of (or better than) 2.2 Å and an R-factor below 20%. A higher resolution of the X-ray data usually provides a better fit and results in a lower R-factor.
The R-factor tells us how good the fit of the structural model to the X-ray data (the electron density) is. The R-factor and resolution are probably the two most central parameters for the assessment of the quality of the structure.
Apart from the coordinates, the file also contains essential information on the method used to solve the structure, the parameters related to the quality of the X-ray data (like resolution), as well as the symmetry operations for the specific space group of the crystal, the quality of the model geometry (deviations of bond lengths, bond angles and torsion angles from ideal values), secondary structure content, description of missing regions in the structure (a result of weak electron density due to flexibility/disorder in the structure).
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