Dear all,
Please anyone give me any advice on the problem below.
Diffraction spots not so bad, collected by HKL2000 to 2.2A. Cell parameter is
a=99.958, b=99.958, c=197.237, Judged by clear systematic absence l=6n and no
mm on hk0, space group P61 or P65, that expects two molecules of 411aa in AU.
Rsym = 7.1, redundancy = ~11. Strangely, plots of reciprocal space show strong
diffractions on h, k, 7n plane, and significantly weak ones or no diffraction
on h, k, 7n+1 and h, k, 7n-1 plane. Of course there are some exceptions, but
this diffraction pattern goes to high resolution with ~35 A2 of Wilson B
factor.
Cumulative intensity distribution plot of TRUNCATE shows acentric observation
curve is much higher than theoretical, and centric observation is lower (half
of theoretical)(fig). This phenomena is quite similar seen in this ccp4bb, for
example, recent case in Qiang Chen wrote at April 3 2008
I started CNS molecular search using a know structure with 40 % identity,
found two solution structure which are not overlap each other. These are
related to pseudo-two fold axis parallel to c. Both makes 61 screw axis along
to c, forming like a double helix.
Molrep found same solution and also showed pseudo-translation vectors.
Peak 1: trans.vector /ort/ : 0.000 0.000 84.717
trans.vector /frac/: 0.000 0.000 0.430
<= 3/7
Peak 2: trans.vector /ort/ : 0.000 0.000 27.783
trans.vector /frac/: 0.000 0.000 0.141
<= 1/7
Peak 3: trans.vector /ort/ : 0.000 0.000 4.895
trans.vector /frac/: 0.000 0.000 0.025
I made model structures created by modeller and started refinement by CNS and
refmac. 2fofc map clearly showed density for 70% of the model. But additional
model building and refinement process could not drop R/Rfree (43/48) any more.
Messy and chopped densities (>3 sig.) are still lying neighbor to the
molecules in fofc map. Some of the density are traceable as a strand and a
helix. But about 20% of the density are crushing to the refined models.
I think that this is a bad case of pseudo-translation generated 3 vectors X 2
molecules along c* axis, but this is not twining. Is my recognition correct?
Please give any suggestion how to overcome this situation by handling this
data, or controlling crystal growth.
Any suggestions will be appreciated.
Kama
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Katsuhiko Kamada, Ph.D.
Senior Research Scientist of
Chromosome Dynamics Laboratory
RIKEN Discovery Research Institute
Bioscience building # N-255,
2-1 Hirosawa, Wako, Saitama 351-0198
JAPAN
E-mail: [log in to unmask]
Phone: +81-48-467-9532
Fax: +81-48-462-4673
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