Hi Jorge,
The strong h, k, l=2n and weak h, k, l=2n+1 pattern suggest pseudo body
centering. Does the off-origin Patterson peak lie at/near 0.5 0.5 0.5?
You could get pseudo body centering if an NCS 2-fold lies parallel to a
crystallographic 2(1) or 6(3) screw axis, with the NCS 2-fold a quarter
(not half) of a unit cell distant from the crystallographic axis.
The fact that you get good merging statistics in P622 even at the high
resolution limit suggests to me that you either have that space group or
a lower symmetry subgroup with a nearly 0.5 twin fraction.
Even if you figure out completely what your pathological crystal
conditions are it may be hard to refine the structure properly. In some
cases crystals can snap from a pseudo- to a proper crystal by adding the
right additive. This may be worth trying while you break your head on
this case.
One problem is that whenever you make a model that obeys the pseudo body
centering you are going to get a significant R-factor and correlation
coefficient, even if the actual model is wrong. If you get a clear
rotation function solution, which is not affected by the pseudo
translation, it may still work but otherwise it could be hard to know if
you got the right solution or not. Trying a whole bunch of rotation
function solutions and see which one will refine to a significantly
lower R-free is one thing to try.
Bart
Jorge Iulek wrote:
Dear all,
Please, maybe you could give some suggestions to the problem below.
1) Images show smeared spots, but xds did a good job integrating them.
The cell is 229, 229, 72, trigonal, and we see alternating strong and
weak rows of spots in the images (spots near each other, but rows more
separated, must be by c*). They were scaled with xscale, P622 (no
systematic abscences), R_symm = 5.3 (15.1), I/sigI = 34 (14) and
redundancy = 7.3 (6.8), resolution 2.8 A. Reciprocal space show strong
spots at h, k, l=2n and weak spots at h, k, l=2n+1 (I mean, l=2n
intensities are practically all higher than l=2n+1 intensities, as
expected from visual inspection of the images). Within planes h, k,
l=2n+1, the average intensity is clearly and "much" *higher at high
resolution than at low resolution*. Also, within planes h, k, l=2n, a
subjective observation is that average intensity apparently does not
decay much from low to high resolution. The data were trucated with
truncate, which calculated Wilson B factor to be 35 A**2.
2) Xtriage points a high (66 % of the origin) off-origin Patterson peak.
Also, ML estimate of overall B value of F,SIGF = 25.26 A**2.
3) I suspect to have a 2-fold NCS parallel to a (or b), halfway the c
parameter, which is "almost" crystallographic.
4) I submitted the data to the Balbes server which using
pseudo-translational symmetry suggested some solutions, one with a good
contrast to others, with a 222 tetramer, built from a structure with 40
% identity and 58% positives, of a well conserved fold.
5) I cannot refine below 49 % with either refmac5, phenix.refine or CNS.
Maps are messy, except for rather few residues and short stretches near
the active site, almost impossible for rebuilding from thereby. Strange,
to me, is that all programs "freeze" all B-factors, taking them the
program minimum (CNS lowers to almost its minimum). Might this be due to
by what I observed in the reciprocal space as related in "1" ? If so,
might my (intensity) scaling procedure have messed the intensities due
to their intrinsic "property" to be stronger in alternating planes ? How
to overcome this ?
6) I tried some different scaling strategies *in the refinement step*,
no success at all.
7) A Patterson of the solution from Balbes also shows an off-origin
Patteron at the same position of the native data, although a little lower.
8) Processed in P6, P312 and P321, all of course suggest twinning.
I would thank suggestions, point to similar cases, etc... In fact,
currently I wondered why refinement programs take B-factor to such low
values
Many thanks,
Jorge
--
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Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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