Re: [phenixbb] on determination whether a protein is a monomer or complex by phenix

Hi Smith, Your solvent content is most likely the 66% one (if you have diffraction to about 1A there's a chance it could be 33%.....in which case try to solve it with Balbes (ccp4)). You can not tell what the crystal packing is like until you solve the structure! Even if you know how many molecules you have in your a.s.u. you can not tell if the contacts are formed because of crystal packing or oligo formation! Its much better to look at your protein in solution for this (as i said before!) Cheers, val On 7 July 2015 at 03:17, Smith Liu wrote:

Dear Valerie and all,

My space group is I422 (attached image for I422). There are 2 solutions for Mathews coefficient, one is solvent content 66.76%, the other is 33.52%. Based on this message and the attached images, how can we know whether my protein is a monomer (for example, monomer protein only exist in the "+" position), a tetramer (or crystal packing as a "tetramer", each chain exist in the "+" position, and each chain so close to each other so that they contact each other and a tetramer forms), a 8-subunit protein complex (or crystal packing as a " 8-subunit protein complex ", each 2 chains exist in the "+" position, and each 2 chians so close to each other so that they contact each other and a 8-subunit protein complex form)?

I am looking forward to getting a reply from you.

Best regards.

Smith

At 2015-07-07 00:34:32, "Valerie Pye" wrote:

Hi Smith,

I'm fairly sure you can not tell the oligomeric state of your protein from an mtz and your sequence. What you can do is calculate the Matthews co-efficient with your given unit cell parameters and size of monomer to see how many copies of your monomer you may have in the a.s.u. The difficulty lies in the fact that if say you have 4 copies of your protein in the a.s.u - this doesn't necessarily mean you have a tetramer - they could be 4 monomers related by n.c.s - or 2 dimers.... Is it possible to solve your structure? Then you confirm your space group and number of molecules in the a.s.u. - then look at the area of contact between monomers to see if they are likely to be because of multimerisation or crystal packing.

Totally agree with Tim that a better way (which you'd probably want to do to back-up a multimeric crystal structure) is by SEC or native PAGE. You could also try SAXS, SEC-MALS, EM, or DLS depending on the size of protein you're looking at. You'd also want to know that you have a clean oligomer and not an aggregate ;)

Good luck,

val

On 6 July 2015 at 12:21, Smith Liu wrote:

...

Dear Tim,

I mean based on the mtz file, can I know whether I will get a PDB file of a monomer or dimer, or trimer, or tetramer or oligomer?

Best regards.

Smith

At 2015-07-06 18:14:03, "Tim Gruene" wrote:

...

Dear Smith,

I would say that size exclusion chromatography or native PAGE are better experimental techniques than crystallography for this type of question.

Best regards, Tim

On 07/06/2015 11:20 AM, Smith Liu wrote:

...

Dear All,

Suppose I have got a mtz file, and I know the aa sequence of the protein from which I got the crystal and the corresponding mtz file, will you please tell me which phenix function (program) can tell me whether my protein crystal was formed by protein monomer or by protein complex, and if formed by protein complex, how many subunits existing in the complex?

Best regards.

Smith

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