Hi all,
I am trying to refine a structure to about 2.0A. Indexing in HKL2000 indicates the protein crystallized in P2 with unit cell lengths (a1=67.5, b1=58.8, c1=98.9) and angles (alpha1=90, beta1=101.5, gamma1=90). Molecular replacement with Phaser yields a solution in P1 21 1 with four molecules in the AU. Successive rounds of refinement lead to good quality maps with chemically appropriate packing of symmetry-related molecules. However, TLS and restrained refinement lead to continuing drops of Rfactor (around 20%, depending on weighting) but the stalling of Rfree around 27%.
When the dataset is processed in P1, the unit cell has the dimensions (a=58.7, b=67.4, c=98.9, alpha=78.5, beta=89.9, gamma=89.9) and Phaser finds 8 molecules in the AU. Structure refinement for this scenario is ongoing, and it has yet to be seen whether this leads to improvement of the statistical parameters.
I have solved other structures of this protein in complex with different substrates. One such structure was successfully solved in P1 21 1 with two molecules in the AU with the unit cell lengths (a2= 47.3, b2=58.9, c2=67.6) and angles (alpha2=90, beta2=99.2, gamma2=90). Interestingly, these dimensions are highly similar to those of current structure, although a1 is equivalent to c2, and c1 is nearly double a2.
I have run phenix.xtriage on the P2 scaled data, and the Patterson Analysis indicates that translational-pseudosymmetry is a posibility in my case. Alternatively, phenix.xtriage on the same dataset processed in P1 indicates the same translational-pseudosymmetry, but also suggests the presence of a pseudomerohedral twin. I am not sure if this twin simply relates the dataset to the higher symmetry P2 group. The sections of both log files pertaining to these analyses are copied below- sorry for all the text!
At this stage, I am wondering what the next steps. Specificity, is this data suspicious for having pseudotranslational symmetry or twinning? If so, what should be my next steps to troubleshoot this problem? Any suggestions would be appreciated.
Thanks in advance,
Keith
______________________________________________________________________________________________
P2 PROCESSED DATA
Patterson analyses:
------------------
Largest Patterson peak with length larger than 15 Angstrom
Frac. coord. : 0.000 0.000 0.500
Distance to origin : 49.477
Height (origin=100) : 42.327
p_value(height) : 2.073e-04
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 2.073e-04.
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)
( 0.000, 0.000, 0.500 ) : 42.327 (2.073e-04)
( 0.111, 0.000,-0.476 ) : 8.908 (2.385e-01)
If the observed pseudo translationals are crystallographic
the following spacegroups and unit cells are possible:
space group operator unit cell of reference setting
P 1 21 1 (a,b,2*c) x, y, z+1/2 (67.48, 58.78, 49.48, 90.00, 101.49, 90.00)
_______________________________________________________________________________________________
P1 PROCESSED DATA
##----------------------------------------------------##
## Twinning Analyses ##
##----------------------------------------------------##
Using data between 10.00 to 2.82 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
-------------------------------------------------------------------------------
| Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law |
-------------------------------------------------------------------------------
| PM | 2-fold | 0.256 | 0.186 | 0.003 | h,-k,-l |
-------------------------------------------------------------------------------
M: Merohedral twin law
PM: Pseudomerohedral twin law
0 merohedral twin operators found
1 pseudo-merohedral twin operators found
In total, 1 twin operator were found
Details of automated twin law derivation
----------------------------------------
Below, the results of the coset decomposition are given.
Each coset represents a single twin law, and all symmetry equivalent twin laws are given.
For each coset, the operator in (x,y,z) and (h,k,l) notation are given.
The direction of the axis (in fractional coordinates), the type and possible offsets are given as well.
Furthermore, the result of combining a certain coset with the input space group is listed.
This table can be usefull when comparing twin laws generated by xtriage with those listed in lookup tables
In the table subgroup H denotes the *presumed intensity symmetry*. Group G is the symmetry of the lattice.
Left cosets of :
subgroup H: P 1
and group G: P 2 1 1
Coset number : 0 (all operators from H)
x,y,z h,k,l Rotation: 1 ; direction: (0, 0, 0) ; screw/glide: (0,0,0)
Coset number : 1 (H+coset[1] = P 2 1 1)
x,-y,-z h,-k,-l Rotation: 2 ; direction: (1, 0, 0) ; screw/glide: (0,0,0)
Note that if group H is centered (C,P,I,F), elements corresponding to centering operators are omitted.
(This is because internally the calculations are done with the symmetry of the reduced cell)
Splitting data in centrics and acentrics
Number of centrics : 0
Number of acentrics : 28180
Patterson analyses
------------------
Largest Patterson peak with length larger than 15 Angstrom
Frac. coord. : 0.000 0.000 0.500
Distance to origin : 49.435
Height (origin=100) : 42.048
p_value(height) : 2.159e-04
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 2.159e-04.
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)
( 0.000, 0.000, 0.500 ) : 42.048 (2.159e-04)
(-0.003, 0.110, 0.479 ) : 6.346 (6.347e-01)
If the observed pseudo translationals are crystallographic
the following spacegroups and unit cells are possible:
space group operator unit cell of reference setting
P 1 (b,c,2*a) x, y, z+1/2 (49.44, 58.74, 67.39, 89.85, 78.46, 89.86)