Yes, that's true: coiled-coils are a nightmare, especially for molecular
replacement! Apart from potential twinning problems, the internal
symmetry and often very tight packing makes it extremely awful for MR
replacement trials. I would recommend to create at least seven models
for molecular replacement, each shifted by one residue along the
coiled-coil helix axis, because of the seven-residue-long
heptad-repeats. Even if there is no overall-bend of the coiled-coil
helix, it will still be difficult.
Anyway, good luck!
Dirk.
Am 26.01.10 12:41, schrieb Phil Evans:
> I would guess that coiled-coil structures might be difficult to solve by MR because of multiple false solutions in a repetitive structure.
>
> There's a lot to be said for experimental phases
>
> Phil
>
> On 25 Jan 2010, at 17:50, Michele Lunelli 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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