Thank you all.
I think i have known the reason for the low occupancy.
First, I co-crystallized the protein and peptide with a molar ratio 1:5. In
this situation, the peptide likely would fully occupy the protein binding
site. But the crystal is hard to freezen, so stepwise freezen method was
used.
> If you assume atomic B-factors of 100 or larger and
> calculate the density, I really can't see how this is possible.
Well, I do. The recipe has been published in NSB as a cautionary tale.
http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf
and there is quite fail-safe away to inves
Dear Jiamu Du,
what were the exact concentrations (Molar values please) of protein and
peptide in the co-crystallization experiment? This may help in
estimating the (possible) occupancy of your peptide.
Jeroen.
JDwrote:
Does anyone know a program can perform the ocupancy refinement?
Or we
Dear all,
Frankly speaking I am having some doubts about this whole
discussion.
1. Apparently, it does not make a difference in R and Rfree
whether the peptide is in the structure or not. This does
suggest that there is very little (if any) information about
the peptide in the data. Righ
Shelx can refine occupancies.
Arti
> Does anyone know a program can perform the ocupancy refinement?
> Or we always only refine B factor to reflect the occupancy?
>
> Thanks
>
>
> On 4/30/07, Eleanor Dodson <[EMAIL PROTECTED]> wrote:
>>
>> Well - it is extremely likely that the peptide is partially
Does anyone know a program can perform the ocupancy refinement?
Or we always only refine B factor to reflect the occupancy?
Thanks
On 4/30/07, Eleanor Dodson <[EMAIL PROTECTED]> wrote:
Well - it is extremely likely that the peptide is partially occupied and
the occupancy may well be < 0.5..
Well - it is extremely likely that the peptide is partially occupied and
the occupancy may well be < 0.5..
But at this resolution you are going to have great difficulty deciding
whether you should have
Occ=1.0
Occ = 0.5
Occ = 0.33
As your Rfactors show it makes very little difference t
Dear All:
According to your suggestion, I have set the peptide's occupency to 0.5. Two
strategies were employed.
1. Direct using Refmac restrained refinement for 10 cycles. The B factor
only drops to around 100. R/Rf did not change, either.
2. Direct CNS B-fator refinemen. The B factor drops to a
Hi Jiamu,
is the high B-value of your protein due to motions, which are not
modeled appropiately ? Which program by the way are you using for
refinement ? Then the TLSMD server might help you here. Monomer or
multimer in the asu ? NCS used, if so checked that they actually follow
NCS and you'
I will try it soon. If it work, I will paste a sumary.
Thanks
On 4/30/07, Jacqueline Vitali <[EMAIL PROTECTED]> wrote:
Hello,
I think it is because the peptide does not have full occupancy. I do
not know if it is OK to fix occupancy to 0.5 and do the refinement.
That would bring temp factor
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