Looking at the P422 data, it look like you have pseudo translational symmetry. Did you try processing this data as I422?
From the P422_xtriage.log:
The full list of Patterson peaks is:
x y z height p-value(height)
( 0.500, 0.500, 0.165 ) : 78.635 (6.634e-07)
( 0.000, 0.000, 0.330 ) : 56.292 (2.795e-05)
( 0.500, 0.500, 0.497 ) : 30.920 (1.207e-03)
( 0.500, 0.500, 0.187 ) : 4.873 (9.347e-01)
If the observed pseudo translationals are crystallographic
the following spacegroups and unit cells are possible:
space group operator unit cell of reference setting
I 4 2 2 (a,b,3*c) x+1/2, y+1/2, z+1/6 (191.70, 191.70, 103.68,
90.00, 90.00, 90.00)
Secondly, for your I4 datasets, if the resoluiton of your
I422_xtriage.log file is correct (2.76 angstroms), then an r=29% and
r-free=34% is not too far off, using the general rule of thumb that a
structure is close to completion when the r-factors are 10 times the
resolution. For example, resolution of 2.7 a r-factor around 27%
should indicate that the structure is close to finished.
Ultimately, it's your manual inspection and judgement (aside from
statistics) that dictate whether you think the structure to be fully
refined.
Hope that helps,
Kelly
*******************************************************
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
*******************************************************
On Mon, May 7, 2012 at 10:50 AM, Zhou, Tongqing (NIH/VRC) [E]
Dear All,
I have collected several dataset for an antibody:antigen complex. It apparently indexed to P4 space group with large cell dimensions of 191.7000/191.7000/311.0540. When I processed as P1 and ran Pointless, it suggested P422 as space group. P4212 gives the best MR solution with 6 mol/ASU (18 chains total ). However, ridigbody and subsequent refinement with TLS could not reduce the r and r-free which stayed at ~48%. Tried to go P4, P222…(12 mol/ASU) with twinning, but the refinement failed due to insufficient computer memory (12 GB), it was also impossible to refine in P1 due to the same reason.
But for some data sets, HKL2000 also gave I4 space group with c axis reduced to 1/3 of that of P4. With the I4 data (~2.7 A resolution), I422 was the best MR space group (1 mol/ASU), the refinement went down to r=29% and r-free=34%, but won’t go down further.
Please advise if it’s possible to use the data
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4609B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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