When we ran into reviewer complaints a while back we referred to Methods
in Enzymology, 277:366-396. I can't lay my hands onto this to verify
the statement, but back then it was good enough to placate the reviewer.
Full QnA with reviewer:
3) Why were only 1% of the reflections included in the test set for the
free R value?
The original publication by Axel Brünger used 10% of the reflections for
the test set, and this became standard practice. However, further
analysis by Axel Brünger indicated that it is the absolute number of
reflections in the test that is important, not the relative size, and he
recommended that a test set size of at least 500 reflections (Methods in
Enzymology, 277:366-396. Accordingly, we conservatively use a test set
of 1,264 reflections, which gives the significant advantage that more
terms can be used in the refinement calculation.
Andreas
Tim Gruene wrote:
On Tue, 17 Jun 2008, Anastassis Perrakis wrote:
been highly correlated with the phase accuracy of the atomic model. In
practice, about 5-10% of the observed diffraction data (chosen at random
from the unique reflections) become sequestered in the test set. The size
of the test set is a compromise between the desire to minimize
statistical
fluctuations of the free R value and the need to avoid a deleterious
effect
on the atomic model by omission of too much experimental data.
I could not find the full text of the 1992 paper.
If I remember correctly (Tassos, you would have found it in the basement
of the EMBL in Grenoble ;-)) Axel Brunger states in the 1992 article
that 500-1000 reflections are sufficient for his purposes of Rfree
calculations.
Tim
