How you choose to make use of (or ignore) crystallographic symmetry comes down to your
view of what constitutes the "best" model for the sample you're studying. How
similar do you believe the molecules are in your crystal? If you describe the model in a
higher symmetry space group, you believe that given the information content of the
diffraction pattern, the molecules are identical. If you describe it using fewer
symmetry operations, you believe the molecules differ in some way. So, how you describe
the symmetry of your crystal comes down to determining the simplest model consistent with
your experimental observations. Ron
On Thu, 21 Oct 2010, Jacob Keller wrote:
I have heard many times that it is a black eye to refine in a lower-symmetry
spacegroup, but I could never really
understand why. The higher symmetry could be considered merely a helpful
theoretical lens to improve signal-to-noise,
and therefore imposing higher symmetry on the data could be seen as a sort of
*leniency* of scientific (or at least
empiric) rigor. I think similarly about using discrete spot intensities rather
than the whole image--we assume Bragg
conditions and neglect certain things about the image between the spots, which
is usually valid, but not always. I
wonder why it is considered maladroit to refine in a lower spacegroup,
then--don't higher spacegroup impose more
assumptions than p1?
Jacob Keller
----- Original Message -----
From: James Holton
To: [email protected]
Sent: Thursday, October 21, 2010 10:55 AM
Subject: Re: [ccp4bb] Regarding space group P1, P21
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 <[email protected]>
To: [email protected]
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
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [email protected]
*******************************************
