Thank you, Edward, for sharing this. I will read through the (extensive)
details of the work.
J.
On 7/22/22 10:25 PM, Edward A. Berry wrote:
As for your second question, whether refining in a lower symmetry
affects the R-factors,
On 7/20/22 10:10 AM, Jorge Iulek wrote:
Related, and a question I mentioned before in this forum: what
if a genuine 2 axis (say , P222 to P2, or even to P1) (I do not mean
this is the case here) is ignored such that one would have doubled
the number of observations but also doubled the number of parameters
to be refined (suppose to exclude NCS in any case). Would one expect
R/Rfree values to be similar in both P222 and P2 (or even P1)? How
much extra freedom would one have besides the twin domain fractions
to refine?
The experiment described here:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg46635.html
addresses this, although it wasn't the main point of that email.
The structures 1CHR and 2CHR are derived from the same crystal. Data
was collected in I4 and 1CHR was published with this space group, and
with the low symmetry data. It was later concluded that the true
space group was I422. The original data was reduced to that space
group and the structure solved again. In the experiment described in
the email referenced above, the model of 2chr was refined using (then)
current phenix.refine. In parallel the 2CHR structure was expanded to
a dimer and refined against the original low-symmetry data.
Because the number of reflections was low (even with 10% free) the
uncertainty in R-free was high, so the refinement was repeated 10
times in each case, with different randomly selected free sets, to get
the average. In each case the refinement was carried out for 50
macrocycles to approach convergence. The R and Free-R values were not
significantly different.
eab
From that email:
2. The deposited structure was refined in I422 10 times, 50 macrocycles
each, with randomly picked 10% free reflections
R: 0.1725±0.0013 Rfree: 0.2507±0.0062 Nfree: 908.9± Nrefl: 9087
3. The structure was expanded to an I4 dimer related by the unused I422
crystallographic operator, matching the dimer of 1chr. This dimer was
refined against the original (I4) data of 1chr, picking free reflections
in symmetry related pairs. This was repeated 10 times with different
random seed for picking reflections.
R: 0.1666±0.0012 **Rfree:0.2523±0.0077 Nfree: 1601.4 Nrefl:16011
4. same as 3 but picking free reflections randomly without regard for
lattice symmetry.
On average 15 free reflections were in pairs, 212 were invariant under
the operator (no sym-mate) and 1374 (86%) were paired with working
reflections.
R: 0.1674±0.0017 **Rfree:0.2523±0.0050 Nfree: 1600.9 Nrefl:16011
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