Re: [ccp4bb] MR on low resolution soaking data.

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: How to fit the crystal structure into the em model(not the real data but the vrml file)
From: junfeng liu jliu {- at -} NIMR {- dot -} MRC {- dot -} AC {- dot -} UK
Date: 2010-06-08

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From: Sean Gay scgay {- at -} UCSD {- dot -} EDU
Date: 2010-06-08

Subject: Re: MR on low resolution soaking data.
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2010-06-08

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 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
>>
>>
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: JLigand Coot link
From: Sean Gay scgay {- at -} UCSD {- dot -} EDU
Date: 2010-06-08