Dear Sir,
Its not a membrane protein. Due to the high
solvent content, it diffracts to a lower resolution
of around 3.5 Ang.
Thank you
Regards
Kavya
> Is it a membrane protein? Membrane proteins often co-purify with
> a belt of disordered lipid/detergent around the part of the protein
> that was in the hydrophobic phase of the membrane. This gets counted
> as "solvent" and as a result I think membrane proteins have on the
> average a higher solvent content than soluble proteins.
> eab
>
> On 09/28/2015 04:42 AM, Kavyashree Manjunath wrote:
>> Dear All,
>>
>> Thank you all for your suggestions. There is a huge
>> solvent cavity inside the crystal. And there are no
>> additional densities in this region to fit a monomer.
>> So as all of you suggested, probably this is an outlier
>> and PHASER solution in right.
>>
>> Thank you
>> Regards
>> Kavya
>>
>>> Hi Kavya,
>>>
>>> The important point here is that the calculator provides
>>> 'probabilities'
>>> and 'estimates' based on the most probable values observed in the PDB.
>>> If
>>> your protein deviates from a number of simple assumptions and 'average
>>> properties' then the predictor must invariably but statistically
>>> correct
>>> assign a low probability for your monomer or assembly.
>>>
>>> In the original calculator,
>>> http://www.ruppweb.org/mattprob/default.html
>>> the output is more verbose and following a suggestion of Dale Tronrud,
>>> emphasizes probability and lists more digits for the probability as not
>>> to
>>> confuse people by stating 0.00 for very low probabilities. Maybe this
>>> can
>>> be adapted in the Phaser output.
>>>
>>> More discussion of the limits of such predictions can be found in the
>>> kernel update paper:
>>> http://scripts.iucr.org/cgi-bin/paper?S1399004714005550
>>>
>>> Best, BR
>>>
>>>
>>> On Mon, Sep 28, 2015 at 12:25 AM, Randy J. Read <[log in to unmask]>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I don't think you would get such low R-factors so readily if you were
>>>> missing half the structure. 73% solvent is unlikely but not
>>>> impossible.
>>>> If
>>>> you look at the packing, is there a connected lattice that could form
>>>> a
>>>> plausible crystal? If your protein is a dimer, is there an
>>>> appropriate
>>>> dimer generates by symmetry?
>>>>
>>>> Another possibility is that there is statistical disorder, if you
>>>> don't
>>>> see plausible packing.
>>>>
>>>> Best wishes,
>>>>
>>>> Randy Read
>>>>
>>>> ----
>>>> Randy J. Read
>>>>
>>>>> On 28 Sep 2015, at 07:54, Kavyashree Manjunath
>>>> <[log in to unmask]>
>>>> wrote:
>>>>>
>>>>> Dear users,
>>>>>
>>>>> I am working on a 25kDa protein. The data was processed in
>>>>> P6122 space group. According to the Matthews coefficient
>>>>> calculated by "cell content analysis" program in CCP4, it is
>>>>> a dimer with a probability of 0.98.
>>>>>
>>>>> -----------------------------------------------------------
>>>>> Nmol/asym Matthews Coeff %solvent P(3.53) P(tot)
>>>>> _____________________________________________________________
>>>>> 1 4.63 73.44 0.02 0.01
>>>>> 2 2.31 46.88 0.97 0.98
>>>>> 3 1.54 20.32 0.00 0.00
>>>>> -----------------------------------------------------------
>>>>> I searched for dimer, but Phaser did not give any solution.
>>>>> but gave a solution when searched for a monomer.
>>>>>
>>>>> One round of refinement with the monomer, resulted in an R
>>>>> and Rfree of 0.26 and 0.32 respectively.
>>>>>
>>>>> Why PHASER is not giving a dimer? What problem could the data
>>>>> have in such cases?
>>>>>
>>>>> Thank you
>>>>> Regards
>>>>> Kavya
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
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>>>
>>>
>>>
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