R factor

Facteur R (Fr). R-Faktor, Übereinstimmungsfaktor (Ge). Fattore R (It). R 因子 (Ja). R-фактор (Ru). Factor R (Sp).

Definition

The term R factor in crystallography is commonly taken to refer to the 'conventional' R factor

$R = {{\sum | F_{obs} - F_{calc} | } \over {\sum |F_{obs} |}}$,

a measure of agreement between the amplitudes of the structure factors calculated from a crystallographic model and those from the original X-ray diffraction data. The R factor is calculated during each cycle of least-squares structure refinement to assess progress. The final R factor is one measure of model quality.

More generally, a variety of R factors may be determined to measure analogous residuals during least-squares optimization procedures. Where the refinement attempts to minimize the deviates of the squares of the structure factors (refinement based on $F^2$), the R factor based on $F^2$ is used to monitor the progress of refinement:

$R(F^2) = {{\sum | F^2_{obs} - F^2_{calc} | } \over {\sum |F^2_{obs} |}}$.

Likewise, refinement based on I can be tracked using the Bragg R factor

$R_B = {{\sum | I_{obs} - I_{calc} | } \over {\sum |I_{obs} |}}$.

Even for refinement based on $F^2$ or I, the 'conventional' R factor may be calculated and quoted as a measure of model quality, in order to compare the resulting quality of models calculated at different times and with different refinement strategies.

The R factor is sometimes described as the discrepancy index.

R factor as a measure of structure quality

Theoretical values of R range from zero (perfect agreement of calculated and observed intensities) to about 0.6 for a set of measured intensities compared against a set of random intensities. R factors greater than 0.5 indicate very poor agreement between observed and calculated intensities, and many models with $R \ge 0.5$ will not respond to attempts at improvement. An early model with $R \le 0.4$ can usually be improved during refinement. A desirable target R factor for a protein model refined with data to 2.5 Å is considered to be $\sim 0.2$. Small organic molecules commonly refine to $R \lt 0.05$. However, the R factor must always be treated with caution, as an indicator of precision and not accuracy. Partially incorrect structures have been reported with R values below 0.1; many imprecise but essentially correct structures have been reported with higher R values.

Weighted R factors

In practice, weighted R factors are more often used to track least-squares refinement, since the functions minimized are weighted according to estimates of the precision of the measured quantity Y: $\sum w (Y_o - Y_c)^2$ (Y being F, $F^2$ or I). The general term for a weighted residual is

$wR = \Big({{\sum |w |Y_o - Y_c|^2|}\over{\sum |wY^2_o}|}\Big)^{1/2}$.

The sum is usually computed over all reflections measured in the experiment. However, occasionally reflections are omitted from the calculation, either because they are believed to result from a systematic experimental error or are recorded with an intensity small compared with background noise. Any such selection may introduce statistical artefacts, and must always be described when reporting R factors.