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
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > This message has been scanned for viruses and
>> > dangerous content by MailScanner, and is
>> > believed to be clean.
>>
>
>
>
> --
> -----------------------------------------------------------------
> Bernhard Rupp (Hofkristallrat a. D)
> 001 (925) 209-7429
> +43 (676) 571-0536
> [log in to unmask]
> [log in to unmask]
> http://www.ruppweb.org/
> -----------------------------------------------------------------
> The hard part about playing chicken
> is to know when to flinch
> -----------------------------------------------------------------
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
|