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Dear Satvik,

 

You only know if the space group is correct AFTER you solved your structure. With an Rwork/Rfree of 0.43/0.48, the space group is likely not correct. The way to solve this is to run MR in all possible space groups. Most, if not all MR programs have an option to do this automatically.

 

For phaser e.g. you have to give the command: SGALTERNATIVE SELECT ALL

If your search model is not too different from the crystallized protein, this should work without a problem. Otherwise, you get into the realm of difficult molecular replacement and that will be a different story.

 

Good luck!

Herman

 

Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Satvik Kumar
Gesendet: Dienstag, 19. September 2017 16:02
An: [log in to unmask]
Betreff: Re: [ccp4bb] doubt regarding MR search model

 

Hello,

Thanks everyone for your explanations.

I have pasted the pointless output to provide more information.

Best Solution:                                  space group P 21 21 21
Laue group probability:                   0.959
Systematic absence probability:     0.818
Total probability:                             0.785
Space group confidence:                0.751
Laue group confidence                   0.951

 

Unit cell:   82.10 100.51 157.11     90.00  90.00  90.00
Also based on L-test, pointless says data does not suggest twinning.
Yes, the R values go down when I refine in both cases. After 20 rounds of restrained refinement using the coordinates generated by monomer as search model, the Rwork and Rfree are 0.43 and 0.48

respectively. Refinement using the coordinates generated by using dimer as search model also results in similar R values. I have attached the plots to show that the R values indeed reduce in both cases.

Is my space group correct? Do I need to reexamine the space group even though the probability is high?

If my space group is indeed correct, how do I decide whether to go ahead with the results generated by the monomer search model or the dimer?

Please share your thoughts.

Thanks,

Satvik

 

On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson <[log in to unmask]> wrote:

You need to provide a bit more information.

First of all about the data processing..

Is the space group correct?

ways of being misled are:

Non-crystallographic translations with a shift of ~0.5 along an axis - say a.  This will generate absences in the odd h 0 0 reflections and can make the space group appear to be P 21 21 21 whilst it is really P 2 21 21..

Perfect twinning can have the same effect. In an orthorhombix space group this can usually only occur if two axes have approximately the same length, but the data processing stats can indicate if that is the case.

Then - re PHASER. The packing rejection criteria may be set too severely - that seems the case for your solution.

Best check on any MR solution is: does it refine - give it 20 cycles of mindless refinement and see if the R and FreeR go down.

Then look at the maps and see if there are obvious corrections to be made..

Eleanor

 

On 18 September 2017 at 14:59, Satvik Kumar <[log in to unmask]> wrote:

Dear Crystallographers,

I am trying to solve a structure in the space group P212121. Based on Matthews coefficient, there are 4 molecules in the asymmetric unit.

Based on my limited reading about using of Phaser, I understand that a single chain should be used as search model even though many copies are present in asymmetric unit. Am I correct?

So when I use a single chain as search model and ask Phaser to search for 4 molecules, Phaser identifies a single solution with a warning "The top solution from a TF rescoring did not pack" and a warning "Search request requires more scattering than defined in composition. Composition increased to accommodate search components". But the final values reported "PAK=2 LLG=1065 TFZ==22.6" indicate that phaser has solved the problem.

Can anyone please explain the meaning of the warning.

When I inspect the arrangement of the chains (attachment), I observe minimal contact between the chains and a large cavity in the center. Can a crystal form this way?

I have also tried using the dimer as search model and asking phaser to search for 2 molecules. Even in this case, Phaser finds a single solution but the warning and the advisory still appear as before. The numbers reported reduce a bit to "PAK=1 LLG=722 TFZ==29.2".

Please help me in understanding these results.

Thanks,

Satvik