You pick the Rfree flags in the high-symmetry space group, and then use
"CAD" with "OUTLIM SPACE P1" to symmetry-expand them to P1 (or whatever
you like).
Things get trickier, however, when your NCS is close to, (bot not
exactly) crystallographic (NECS?). Or if you are simply not sure. The
best way I can think of to deal with this situation is to "road test"
your Rfree:
1) do something that you know is "wrong", like delete a helix, or put
some side chains in the wrong place
2) refine with NCS turned on
3) check that Rfree actually goes up
4) un-do the "wrong" things
5) refine again
6) check that Rfree actually goes down
7) try again with NCS turned off
Remembering these timeless words of wisdom: "Control, Control, you must
learn CONTROL!" -Yoda (Jedi Master)
-James Holton
MAD Scientist
On 10/21/2010 8:46 AM, Christina Bourne wrote:
Dear all,
How would one properly select reflections for R-free in these
situations? Presumably if the selection is done in P1 then it mimics
twinning or high NCS, such that reflections in both the work and free
set will be (potentially?) related by symmetry.
-Christina
------------------------------------------------------------------------
*From:* Mohinder Pal <m...@soton.ac.uk>
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Thu, October 21, 2010 7:05:42 AM
*Subject:* [ccp4bb] Regarding space group P1, P21
Dear CCP4BB members,
I have solved a protein-drug complex structure in P21212 space group.
In this structure, the drug molecule is falling on the two-fold
symmetry axis having averaged electron density with 0.5 occupancy. We
tried a lot to crystallize this protein-drug complex in different
space group but no success so far. I have tried to solve the same
data in space group P1 (statistics are fine as I have collected data
for 360 degree). The map looks even better with one conformation for a
drug. Interestingly, then I reprocessed the same data using imosflm in
P21 space group which have penalty 1 compared to 4 for P21212. The
structure in P21 is also refining well (with one conformation of the
drug compound without symmetry axis at the ligand position). The
question is , is it a good practice to solve this structure in P1 and
P21 even if the data has higher symmetry?
Secondly, I have been advised that I have to be careful to refine
structure in P1 as there will be problem regarding
observation/parameter ratio if I add too many water molecules. What
will be the case if the electron density present for water molecules?
I can put restrains to protein structure but I am just curious to
know one restrain equals how many observations.
I look forward to hear your suggestions.
Kind regards,
Mohinder Pal
