Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.

By A. Brunger. 1992

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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “For cross-validation, Rfree is calculated on a subset of the data (typically about 2000 reflections) that are not used in refinement (Brünger, 1992).”
Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “…procedure fails to produce optimal weights, a more time-intensive automatic weight-optimization procedure may be used, as originally described by Brünger (1992) and further adopted by Afonine et al. (2011), in which an array of wxcscale or wxuscale values is systematically tested in order to…”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “In crystallography, the model-to-data fit is quantified by crystallographic R and Rfree (Brunger, 1992) factors, which are global reciprocal space metrics.”
A short history of SHELX. (2008, methodology): “Although some facilities such as conjugate-gradient refinement (Konnert, 1976), the free R factor (Brunger, 1992) and non-crystallographic symmetry (NCS) restraints (Usón, Pohl et al., 1999) were added specially for macromolecular refinement, there are also features missing that would be desirable…”
Averaged kick maps: less noise, more signal…and probably less bias (2009, methodology): “…improvement towards reducing map bias was the computation of weighting terms (m and D) using a subset of reflections set aside for cross-validation (‘test’ reflections; Brünger, 1992) and used for estimation of phase errors (Lunin & Skovoroda, 1995; Pannu & Read, 1996; Urzhumtsev et al., 1996).”
Model validation: local diagnosis, correction and when to quit (2018, background): “In less ideal circumstances the contacts act like a super-sized Rfree, assessing the heavier atom positions by the fit of the unseen other half: the H atoms.”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “Running AutoBuild without NCS and with torsion NCS produces final models with similar R factors, with the torsion NCS model having a slightly smaller Rfree–Rwork gap (Brünger, 1992), consistent with a less overfitted model.”
The PDB_REDO server for macromolecular structure model optimization (2014, background): “An additional improvement concerns the calculation of Rfree (Brünger, 1992) in cases where the test set of reflections used for calculation of Rfree is very small and stochastic effects can cause Rfree for a particular set of test reflections to be substantially (up to several percentage points)…”