[phenixbb] Is it possible to do Molecular Replacement for synthesized "small" molecule X-ray data?

Randy J. Read rjr27 at cam.ac.uk
Tue Dec 8 12:18:17 PST 2009

Dear Yves,

That's probably getting close to the limit of the ratio of the size of the 
molecule to the resolution, which is one of the main things determining 
whether molecular replacement will work. At 1.5A, you'd have to have a 
pretty accurate model of the structure as well (i.e. RMSD signficantly 
under 1A, at a guess). Another problem with molecular replacement for small 
molecules is that small molecule crystals tend to be tightly packed, which 
makes things somewhat harder. Nonetheless, I've done test calculations in 
the past that show it can work.

One thing you should watch out for: Phaser only accepts atoms that are 
given as ATOM records in a PDB file, so if you have HETATM records, those 
atoms will be rejected.

If you'd like to send the logfile from Phaser (preferably off-line), I 
could take a look at it.


Randy Read

On Dec 8 2009, Yves Wang wrote:

>Hi PHENIX users,
>We've got a synthesized molecule, called Cucurbit[7]uril, molecular 
>weight 1163 Da. We were able to grow crystals of cucurbit[7]uril with 
>one of its ligand. This crystal diffracted to 1.5A at our X-ray machine. 
>The dilemma is that, at this resolution, we can't use small molecule 
>crystallography softwares to solve the structure (correct me if I'm 
>wrong, we need at least 1A resolution?), while macromolecular X-ray 
>softwares are really not designed for synthesized molecules.
>We have collected diffraction data of this crystal with decent quality. 
>So I'm  wondering if there's any way we can put a known crystal 
>structure of cucurbit[7]uril and solve the structure of the complex. We 
>have tried AutoMR but the solution is not very encouraging.
>Any suggestion will be gratefully appreciated.

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