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

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

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From: Chun Luo chun {- at -} ACCELAGEN {- dot -} COM
Date: 2010-06-07

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From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2010-06-07

Subject: Re: MR on low resolution soaking data.
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2010-06-07

You haven't given much detail to work with so I can only
guess about your problem. A Wilson B of 20 for a 4 A data set
is ridiculous, but the uncertainty in the Wilson B calculation
at 4 A is enormous, so what might be a more reasonable statement
would be to say your Wilson B calculates to 20 +_ 300 A^2 and
the true value would be in that range. I don't think a precise
Wilson B is important for MR so I wouldn't worry about it.

An R value of .7 after MR is very large. Its size implies
a systematic problem with your model - I would be looking for
a second monomer. You haven't said anything about the structure
of your monomer. Often a ligand will bind in the cleft between
two domains, and the domains move relative to each other upon
binding. You may have to perform separate searches for each
domain or construct a range of trial models with different
angles between the domains.

Don't worry about the ligand until you solve the protein
structure. Whether you see it in the end will depend on how
big it is and how good your 4 A data are. Of course, it's
possible that it doesn't bind at all.

Dale Tronrud

On 06/07/10 12:17, yang 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

CCP4bb navigation

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

Previous message:
Subject: Re: insect cell media
From: Chun Luo chun {- at -} ACCELAGEN {- dot -} COM
Date: 2010-06-07

Next message:
Subject: New Version of the Protein Geometry Database Operational
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2010-06-07