There are a good many coiled coil models available. I suggest you search
the pdb for more models yourself, or let a program like BALBES do it for
you and do the MR searches as well.
IF you get a faint hit (usually marked by both R and rfree dropping a
few % on refinement) then Arp-warp or buccaneer may kick in and do some
automated rebuilding.
Eleanor
wu donghui wrote:
Two cents are added here.
First, try P2 as somethimes systematic absence along b axis is misleading
due to weak diffraction or pseduo translation.
Second, try P1.
Good luck,
Donghui
On Tue, Jan 26, 2010 at 1:50 AM, Michele Lunelli <efu...@yahoo.it> wrote:
Dear all,
I am trying to solve a structure at 2.05 A resolution by molecular
replacement. The space group
seems to be P21, with unit cell dimension 52.63, 29.43, 104.970 and beta =
95.60.
Only one copy of the protein should be present in the asymmetric unit, with
58% of solvent content.
The search model used for MR is a truncated construct of the same protein,
comprising more that 60%
of the residues. However, no convincing MR solution is found (I used
phaser, molrep, epmr and also
mr.bump). No solutions refine to R and Rfree lower than 51-52%.
The CCP4 documentation about twinning states that "Monoclinic with na + nc
~ a or na + nc ~ c can be
twinned". This is not clear to me, but I have c = 2a, and therefore n =
2/3.
Nevertheless all the tests run by ctruncate (and sfcheck) exclude twinning.
The observed cumulative
distribution for |L| almost overlap the expected untwinned, and the
observed cumulative intensity
distribution is not sigmoidal at all (actually it is growing faster that
the theoretical). Also the
acentric and centric moments exclude twinning, for example the acentric:
<E> = 0.858 (Expected value = 0.886, Perfect Twin = 0.94)
<E**3> = 1.442 (Expected value = 1.329, Perfect Twin = 1.175)
<E**4> = 2.438 (Expected value = 2, Perfect Twin = 1.5)
Both ctruncate and sfcheck found a pseudo-translation vector:
ctruncate (0.050, 0.000, 0.957), ratio 0.23
sfcheck (0.954, 0.000, 0.040), ratio 0.218
However a second copy cannot be present in the asymmetric unit (there would
be 16% of solvent
content). Since the protein is expected to form a coiled-coil, I think that
the detected
pseudo-translation arises from the helices.
Alternatively, it is possible that the space group is wrong? And if so, how
can I figure out the
correct one?
Thank you in advance,
Michele
