Refinement R Factors

Searches for structures in the specified resolution range. A histogram icon next to the search box links to a histogram that shows the distribution of resolution in the PDB.

Searches for structures in the specified R factor range. R factor is the measure of the agreement between the structural model and the experimental diffraction data. When solving the structure of a protein, the researcher first builds an atomic model and then calculates a simulated diffraction pattern based on that model. The R factor measures how well the simulated diffraction pattern matches the experimentally-observed diffraction pattern. A totally random set of atoms will give an R factor of about 0.63, whereas a perfect fit would have a value of 0. Typical values are about 0.20. See the "Looking at Structures: Resolution" page (here) for more details.

Note: non-diffraction methods such as NMR do not have a resolution specified.

The R factor search supports four types of metrics:

  • R observed - Residual factor R for reflections that satisfy the resolution and observation limits. This quantity includes reflections set aside for cross-validation in a "free" R-factor set. Residual factor R for reflections that satisfy the resolution and observation limits.
  • R all - Residual factor R for all reflections that satisfy the limits established by high and low resolution cut-offs. It includes reflections which do not satisfy the sigma cutoff criteria as well as those set aside for cross-validation in a "free" R-factor set.
  • R work - Residual factor R for reflections that satisfy the resolution and observation limits and that were used as the working reflections in the refinement. This quantity does not include reflections set aside for cross-validation in a "free" R-factor set.
  • R free - Residual factor R for reflections that satisfy the resolution and observation limits and that were excluded from refinement to be used for cross validation in a "free" R factor set. R free is a less biased metric, and is typically higher than an R work. If R free is significantly higher than the R work, the structural model may be over fitted.

Examples

  1. Search for structures with an R free values between 0.18 and 0.24

    "R free": Enter "Between: 0.18 and 0.24

  2. Search for structures with an R free value of up to and including 0.22.

    "R free": Leave the left box empty and enter 0.22 into the right box