Okay, I weigh in on the R factor issue...
The free R that we calculate is only an estimate of the "true free
R". What we really want to know is what would the R value be if there
there was no "bias" to the atomic model. We make this estimate by
pulling a subset of the data out of the refinement. If you pull out a
different subset you will get a somewhat different "free R estimate".
If you run a lot of refinement with different subsets you will get a
distribution of "free R estimates" and that distribution will have a
standard deviation. The smaller the number of reflections in the subset
the larger that standard deviation will be.
One shell of data will have only a few reflections so the standard
deviation will be large and a particular instance may very well have a
value for the "free R estimate" that is smaller than the working R,
particularly when the overall R values are similar as in your refinement.
Dale Tronrud
On 9/19/2022 11:30 AM, Prasun Kumar wrote:
Hi All:
I have collected a dataset for a crystal of a 30 residues long helical
peptide that makes a trimer in the solution. I also solved the structure
to get a trimer. My issues start when I start preparing for a deposition.
Details about the data:
space group: I 21 3
Resolution: 1.6
Current Rfree/ Rwork: 0.21/0.19
Problems:
According to Aimless, Multiplicity: *33.9*, and I understand that the
value should be less than or equal to 20. Does it mean that I have a lot
of random noise or ice rings or something similar?
For the inner shell, R work is also *higher* than R free.
Please guide me in solving the above issue.
Thank You
Prasun
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