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 <[log in to unmask]> 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
>>
>
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