Dear Eleanor,
Yes the native is a dimer and we did the search using the dimer as a
model but we had similar results (i.e. all programs find one molecule).
The graphs from TRUNCATE show rather "normal" and I am attaching a gif
file with the plot for the cumulative intensity.
As for pseudo-translation running the "Analyse Data for MR" option in
ccp4 in the patterson map we are getting a significant peak at
fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we need
to apply this pseudo translation to the solution we are getting from
molrep ?
many thanks
Demetres
P.S. I will summarize for the members of the list all the suggestions I
will get at the end
Eleanor Dodson wrote:
> You dont say whether the molecules in the native cell form a dimer -
> if so I would search with that (you may need to turn off the packing
> search)
>
> Or whether there is a pseudo translation vector in the mutant form..
>
> Or what the data analysis graphs from TRUNCATE show - are they "normal"?
>
> Eleanor
>
> Demetres D. Leonidas wrote:
>> Dear all,
>>
>> we have encountered a problem in solving one mutant structure. The
>> mutant protein crystallizes in the same space group as the native
>> (C2) but the unit cell dimensions are different. These for the native
>> structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4
>> 32.3 107.0 90 125.7 90. As a result the mutant structure has four
>> molecules in the asymmetric unit while the native had two. When we
>> run molecular replacement all programs (CNS, molrep, and amore) find
>> only two molecules. Phaser finds four but when we try to refine the
>> Rfree does not drop below 0.44 if we use four molecules and 0.53 if
>> we only use two no matter how well we built the molecule and
>> regardless of any addition of water molecules (the resolution of the
>> data is 2.1). The interesting thing is that in the electron density
>> map we can clearly see density for a substrate analog that was
>> included in the crystallization media. Do you thing that we have a
>> case of twinning here ? We have to mention that Tod Yates served did
>> not indicate any perfect merohedral twinning (partial merohedral
>> twinning for this space group is not possible).
>>
>> We would appreciate any comments
>>
>> Many thanks
>>
>> Demetres
>>
>
>
--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
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