[phenixbb] is derivative data useful for looking for the missingpart of the model?

[fn1 at rice.edu]

Hi Jacob,

The size for the monomer of protein is 18 kd, and it forms a trimer.  
But in the current model, the monomer becomes two fragment. The  
missing connection part happens to be a loop containing a very short  
helix (8-10 residues) and one disulfide bond as deduced from its  
homologue crystal structure.

We did run the gel for the crystal, but it looks same.

Fengyun


引用 Jacob Keller <j-keller2 at md.northwestern.edu>：

>
>
>> Hi Fengyun,
>>
>> How have you determined whether you in fact have the full-length  
>> protein in your crystals? It sounds like, from your statistics,  
>> that everything is already modelled--it seems hard to believe that  
>> 80% of the whole protein would give such good R values. Do others  
>> agree?
>>
>> You could run some of your crystals on a gel next to a sample which  
>> is known to be full-length, and you could get the answer.
>>
>> Jacob
>>
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> Dallos Laboratory
>> F. Searle 1-240
>> 2240 Campus Drive
>> Evanston IL 60208
>> lab: 847.491.2438
>> cel: 773.608.9185
>> email: j-keller2 at northwestern.edu
>> *******************************************
>>
>> ----- Original Message ----- From: <fn1 at rice.edu>
>> To: <phenixbb at phenix-online.org>
>> Sent: Tuesday, June 15, 2010 5:59 PM
>> Subject: [phenixbb] is derivative data useful for looking for the  
>> missingpart of the model?
>>
>>
>>> Hi everyone,
>>>
>>> I got a partial model, consisting of 80% of the whole molecule,  
>>> from  the molecular replacement. The native data reflects to 2.3  
>>> A, and now  the R/Rfree= 0.22/0.28. My problem is that the missing  
>>> part of the  model is important for us, but there is not any  
>>> density for this  region now.
>>>
>>> Meantime, we have several heavy atom derivative data. My question  
>>> is that if refine the model against the derivative data, will the  
>>> heavy atom appear in the difference map if existing? Any  
>>> suggestions on how  to use the derivative data to locate the  
>>> missing part of model?
>>>
>>> Thanks in advance!
>>> Regards,
>>> Fengyun
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>
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