Dear Sir,
I have labeled it rightly. When I was trying to refine
using the method I mentioned it was giving some less than 1
while some more than 1 as occupancy. I am trying to match with
the peaks now.
Thanking you
With regards
M. Kavyashree
> Dear Kavyashree,
>
> Did you properly label the dual positions as alternate positions (same
> residue number and with A and B added just in front of the residue name)?.
> Also, did the occupancies sum up to less then 1, which makes perfect
> physical sense, or to more than 1? At 2.35 Å and with a partially occupied
> dual cadmium positions, you cannot expect miracles from the refinement
> programs. If the sum is more than 1, I would round off the occupancies to
> some sensible values with a sum of 1 and fix them for the rest of the
> refinement.
>
> Best regards,
> Herman
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> ka...@ssl.serc.iisc.ernet.in
> Sent: Wednesday, May 11, 2011 12:00 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] High B-factor for metal
>
> Dear Sir,
>
> The resolution is 2.35Ang. I was trying to refine Cadmium occupancy
> using the option of "SAD data directly" in refmac (as it cadmium gives
> anomalous signal at 1.54179 wavelength) and then use the obtained
> occupancy of those atoms to refine in usual way. It used to to refine
> occupancies of both cadmium and sulphur in (SO4) which is present in
> the structure, but 2 of the cadmium appears to have dual occupancy
> (which was confirmed as water added as a coordinate sphere used to
> come closer than 2.0 ang after refinement, so I tried giving 2
> occupancies instead). After occupancy refinement as stated above, they
> were not summing up to 1, so I had doubts whether to continue this
> method or not.
>
>
> Thank you
> With regards
> M. Kavyashree
>
>
>> Dear Kavyashree,
>>
>> I expect that you have a low-occupancy cadmium ion bound. If your
>> resolution is not too low, say better than 2.5 Å, I would try to
>> refine the occupancies of all cadmium ions. They are so big that it
>> should work.
>> If this does not work, you can make a rough estimate of the occupancy
>> by using the scroll button in coot. If the electron density of the
>> "regular"
>> cadmiums disappears at say 3 sigma, and of your high-Bfactor cadmium
>> disappears at 1 sigma, you could set the occupancy of the latter to
>> 0.3 and see how the cadmium behaves during refinement. At low
>> resolution occupancies and Bfactors are to a certain extend linked,
>> and errors in your estimate of the occupancy will be compensated by the
>> Bfactor.
>>
>> Good luck,
>> Herman
>>
>>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> ka...@ssl.serc.iisc.ernet.in
>> Sent: Wednesday, May 11, 2011 11:30 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] High B-factor for metal
>>
>> Dear users,
>>
>> I have refined a structure in R3 with cadmium bound to it, which
>> was present in the crystallization condition. There are 2 chains in
>> the asu. The structure is twinned. R and Rfree is around 22% and 28%.
>> One of the cadmium has extremely high B-factor of 127, I tried
>> replacing it with water, but there were positive peaks appearing after
>> refinement, no other components in the protein buffer or
>> crystallization condition fit there. and there are 2 glutamate
>> residues in the interaction distance of "X" that come in that
>> position. So kindly suggest me whether I need to continue with cadmium
>> ion assuming that its occupancy is low, or any other options are there?
>>
>> Thanking you
>> With regards
>> M. Kavyashree
>>
>>
>>
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