If the structure factors are available for the original protein you can
use ALMN to check if there is an agreement between
the two data sets.

(Very old technology but a useful trick)

Other things to check - Does the crystallographic 2fold in P43212
generate a tight dimer?

is there a non-crystallographic 2fold  or a non-cryst translation in the
P2 21 21 crystal?

(If so maybe you should search with the P43212 dimer..)

I would expect the MR to give a solution even if your molecule is
truncated. You will need to turn off the packing checks but there still
should be a strong signal.

Eleanor


Lijun Liu wrote:
> The convention for "P22121"s is P21212, which is used by both CNS and CCP4
> and many else, if not all.  The unit cell needs to be reindexed (a-b-c -->
> b-c-a in your case).  Then please try again.  Lijun
>
>
>
>> Thank you for your suggestions.
>> 1. The unit cell of my crystal is 47.41 99.67 114.97 90 90 90 space group
>> P22121, different from PDB structure 64 64 113 90 90 90 P43212, which has
>> the same growth condition.
>> 2. Mathhews_coef indicate my crystal should be dimer if ~30kD. I used all
>> monomer, dimer and tetramer PDB templates and their truncated models, but
>> all high R-factor.
>> 3. My protein has only one domain(ligand binding domain), and there are
>> both
>> structures reported with or without ligand.
>>
>> I think even though my protein was degraded, the structure can be
>> determined
>> due to its remained same sequence.
>> So now do I have to turn to mass spec?
>>
>> 2008/7/8 Zhijie Li <[log in to unmask]>:
>>
>>
>>>  Hi Haitao,
>>>
>>> I need to ask you a few questions first:
>>>
>>> 1. Did you mean you could not solve your structure by molecular
>>> replacement? Did you compare your crystal's unit cell with the PDB file?
>>> Are
>>> they significantly different? If the assymetric unit has more than one
>>> monomer, have you tried doing a molecular replacement search with one
>>> monomer only?
>>>
>>> 2. Can you give us the PDB number so that we can take a look at the
>>> protein? The reason for that is, I suspect that your protein was not
>>> degraded from either end, but only got clipped some where on the surface
>>> -
>>> so the structure is basically unperturbed.
>>>
>>> If the PDB structure turns out to be single-domain, then you should do
>>> your
>>> molecular replacement search with the whole protein. If it is a
>>> two-domain
>>> structure, and one of them is ~20kD, then try use that 20kD domain to do
>>> the
>>> search again.
>>>
>>> R-fac~=0.5 is probably saying that your current solution is totally
>>> wrong.
>>> As I remember, R-factor for a totally radom acentric (for example,
>>> protein)
>>> structure is 0.59.
>>>
>>> Also, Even if you follow the published crystallization conditions, your
>>> protein may still crystallize in a totally different way. But unless the
>>> protein itself has changed its shape (which normally does not happen),
>>> you
>>> should be able to do a molecular replacement.
>>>
>>> If molecular replacement does not work at all, then maybe it is time
>>> to send your sample to mass spec to see what it really is. But I highly
>>> suspect what you need to do now is nothing but to optimize your
>>> molecular
>>> replacement parameters.
>>>
>>> Zhijie Li
>>> Graduate student, Univeristy of Toronto
>>>
>>>
>>>
>>> ----- Original Message -----
>>>
>>> *From:* Haitao ZHANG <[log in to unmask]>
>>> *To:* [log in to unmask]
>>> *Sent:* Monday, July 07, 2008 10:27 PM
>>> *Subject:* [ccp4bb] Truncated protein structure
>>>
>>> Dear all,
>>> I repeated  a protein crystallization which is reported in PDB with the
>>> almost same condition, and got a 2.6A data. But the problem is that I
>>> can
>>> not determine the right phases with neither CCP4 nor CNS.
>>> Then I found the protein in my crystal had been degraded from ~30kD to
>>> ~20kD by SDS-PAGE, but did not know from which terminus it was
>>> truncated.
>>> So I used truncated PDB templates which N-, C- or both terminal were cut
>>> to
>>> fit the length of my shorter protein, and tried many different
>>> templates.
>>> But always high R-factor (~0.5).
>>> With COOT I found the backbone did not fill the electron density map
>>> perfectly.
>>> The only difference of my crystallization condition is 277K(mine)
>>> *vs*295K(reported) in temprature.
>>>
>>> Any suggestions will be appreciated.
>>>
>>>
>>> Haitao ZHANG, Ph.D Student,
>>> Shanghai Institute of Materia Medica,
>>> Chinese Academy of Sciences
>>>
>>>
>>>
>
>
>