Dear All,
Thank you for your help! There do have something needed to be checked
carefully, as you suggested. Peter Zwart
showed me the right way of explore_symmetry_metric, which indicated there is
some relationship between the two
unit cells. I hope it can explain the strange wilsonB and failure of MR. I
will try to reprocess the data later to make sure.
Best wishes
Yang
On Tue, Jun 8, 2010 at 1:57 AM, Eleanor Dodson <[log in to unmask]> wrote:
> The easy Q first:
> Wilson plot B values are very unreliable for 4A data - b=20 is almost
> certainly wrong, but until you have a model to refine it is hard to get a
> proper estimate.
>
> Q2: With a decent model the ligand should show up as a blob, even at this
> resolution. You might have trouble fitting it, but at least you would know
> whether it had bound or not.
>
> Q3: Why the MR doesnt work - I cant answer this..
> Check the data for any serious problems - missing strong intensities can
> mislead. Is the spce group certain?
>
> Is there any relationship between the P212121 and F222 cells?
>
> Eleanor
>
>
> w it ang li wrote:
>
>> Dear colleagues,
>>
>> We are now trying to soak some ligands into a protein, which is about
>> 60kd in size and the structure has been solved
>> before. But the molecular replacement cannot give a right solution. Below
>> is some contrast of the data:
>>
>> Native 2A P212121 monomer
>> Soaked 4A F222 monomer (more than 70% solvent) or dimer(more
>> possible)
>>
>> I wonder if it is possible to find the ligand in the case of such low
>> resolution, provided the ligand is not so small. What facts
>> could probably lead to the failure of MR? Molrep gave a model of monomer
>> but
>> the rfree is as high as 0.7, while phaser could
>> get no result. I tried phenix.explore_metric_symmetry to find the two
>> spacegroups are not compatible, and the Rmerge of the
>> data seems reasonable.
>> One more question is: the wilson B of the data is lower than 20 from ccp4.
>> Is it common for a 4A data? Since I donnot have
>> the experience of handling this low resolution data yet.
>> By the way, any suggestions about refinement methods in low resolution
>> will
>> be appreciated!
>>
>> Best wishes
>> Yang
>>
>>
>
