Dear experts,
I am working on one dataset (2.5A) which was processed using space group
P43212 ( 107.9, 107.9, 313.7; 90, 90, 90).
After running MR with 6 molecules in ASU and one round of refmac, the R factors
are high (38%/45%).
I ran phenix.xtriage and found that translational pseudo symmetry is likely
present. It suggested that the space group is I4122 with the unit cell about
1/3 smaller (I paste the patterson analyses below).
I tried to reprocess the data to get the suggested space group and unit cell
using HKL2000. But the index always gives a long c axis about 313A.
Could you provide any suggestions on how to proceed?
Patterson analyses
------------------
Largest Patterson peak with length larger than 15 Angstrom
Frac. coord. : 0.500 0.500 0.174
Distance to origin : 93.757
Height (origin=100) : 55.763
p_value(height) : 3.018e-05
The reported p_value has the following meaning:
The probability that a peak of the specified height
or larger is found in a Patterson function of a
macro molecule that does not have any translational
pseudo symmetry is equal to 3.018e-05.
p_values smaller than 0.05 might indicate
weak translational pseudo symmetry, or the self vector of
a large anomalous scatterer such as Hg, whereas values
smaller than 1e-3 are a very strong indication for
the presence of translational pseudo symmetry.
The full list of Patterson peaks is:
x y z height p-value(height)
( 0.500, 0.500, 0.174 ) : 55.763 (3.018e-05)
( 0.500, 0.500, 0.500 ) : 51.209 (5.796e-05)
( 0.000, 0.000, 0.326 ) : 32.915 (8.699e-04)
( 0.000, 0.000, 0.348 ) : 18.765 (1.266e-02)
( 0.500, 0.500, 0.151 ) : 11.396 (9.756e-02)
If the observed pseudo translationals are crystallographic
the following spacegroups and unit cells are possible:
space group operator unit cell of reference setting
I 41 2 2 (a+1/4,b+1/4,3*c) x+1/2, y+1/2, z+1/6 (107.94, 107.94, 104.58,
90.00, 90.00, 90.00)
Thanks,
Dan
