OPne type of symmetry that affects R factors is pseudo translation -
then you have many weak reflections and obv. their R factors are likely
to be high. Check the native 4A patterson for this.
So maybe the Rfactors are reasonable..
In this case you also get confusing twinning statistics. For an
untwinned crystal with pseudo translation the 2nd moment is >> 2, so
twinning can reduce it to an apparently acceptable value..
The new release of SFCHECK does a pretty good job in checking this.
And any crystal with point group C/mmm can be reindexed as P2/m with
a~=c and can be twinned..
Use othercell to check this - Phil Evans wrote the program and it SHOULD
be (but isnt) in the new release of CCP4. You can get it from him;
[EMAIL PROTECTED]
Output for your case:
[EMAIL PROTECTED] testing]$ ~/othercell.linux
Type cell >>77 96 50 90 90 90
Type lattice type >>C
Type target cell, or eof (control/D) for no target >>
<<<<<<<<<<<
Input cell: 77 96 50 90 90 90 - Lattice Type C
Lattice point group: C 2 2 2
Lattice cell: 77 96 50 90
90 90
Lattice unit cell after reindexing: 77 96 50 90
90 90
Reindex operator from initial to lattice cell: [h,k,l]
h' = ( h k l ) ( 1 0 0 )
( 0 1 0 )
( 0 0 1 )
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename:
/y/people/emsley/coot/Linux/share/coot/syminfo.lib
List of possible Laue groups
Cell is the cell reindexed into this Laue group
in a 'standard' setting, unconstrained to group
'Deviation' is maximum angular deviation (degrees)
from cell with Laue group symmetry imposed
'Same cell' and 'Other cell' list alternative indexings
'Other cell' lists the cell difference defined as mean square
difference in basis vectors (columns of orthogonalisation matrix)
Alternative indexing schemes which lead to identical or similar
cells are grouped on continuation lines if they are symmetry-related
Laue group a b c alpha beta gamma Deviation ReindexOperator
C m m m 77.0 96.0 50.0 90.0 90.0 90.0 0.00 [h,k,l]
Possible spacegroups:
<C 2 2 21> <C 2 2 2>
****
C 1 2/m 1 96.0 77.0 50.0 90.0 90.0 90.0 0.00 [-k,h,l]
Same cell [k,-h,l]
... [-k,-h,-l]
C 1 2/m 1 77.0 96.0 50.0 90.0 90.0 90.0 0.00 [h,k,l]
Same cell [-h,-k,l]
... [h,-k,-l]
Possible spacegroups:
<C 1 2 1>
****
P 1 2/m 1 61.5 50.0 61.5 90.0 102.5 90.0 0.00
[-1/2h-1/2k,l,-1/2h+1/2k]
Same cell
[1/2h-1/2k,-l,1/2h+1/2k]
...
[-1/2h+1/2k,-l,-1/2h-1/2k]
Possible spacegroups:
<P 1 2 1> <P 1 21 1>
****
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
If you have pseudosymmetry, how do you treat the data? Same as twinning?
I have a 2.3 A dataset that indexes as C2221 with one protein in the
asymmetric unit. I am also able to process the data as P21 (or it may
have been P212121, I don't have my notes with me at the moment), but
with a dimer in the asymmetric unit. The dimer symmetry axis is
crystallographic in C2221 but non-crystallographic in the P21 case.
Either way, the data seem to process equally well, but I can't get
the R_free much below 27%. The same protein with another ligand also
produced C2221 under different conditions. I collected a better
dataset (higher I/Sig, more redundancy) at a different source. In
spite of being better data, now I can't get the R_free below 30%. I
tried running the data through a twinning server on the net but <I^2>/
<I>^2 = 2.0 (no perfect merohedral twinning). The ligand density
looks great, so I can't be far off.
for reference the unit cell is approx [77, 96, 50] Angstroms with 90,
90, 90 degrees.
Am I being too picky about the R_free or is there something wrong
here? Any ideas?
Richard Gillilan
MacCHESS
Cornell
On Jun 1, 2006, at 7:49 PM, James Irving wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
A (very) long shot might be pseudosymmetry - what were the Rmerge
statistics like? How did they compare with monoclinic? A dimer in a
monoclinic space group with non-crystallographic symmetry that closely
approximates orthorhombic crystallographic symmetry might exhibit this
behaviour.
On 01/06/06, Yi Xue <[EMAIL PROTECTED]> wrote:
begin:vcard
fn:Eleanor Dodson
n:Dodson;Eleanor
email;internet:[EMAIL PROTECTED]
tel;work:+44 (0) 1904 328259
tel;fax:+44 (0) 1904 328266
tel;home:+44 (0) 1904 424449
version:2.1
end:vcard
