[phenixbb] Phaser Small Molecule MR

Diana Tomchick Diana.Tomchick at utsouthwestern.edu
Wed May 1 15:07:00 PDT 2019

Why aren’t you using SHELX?


Diana R. Tomchick
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
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Dallas, TX 75390-8816
Diana.Tomchick at UTSouthwestern.edu<mailto:Diana.Tomchick at UTSouthwestern.edu>
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(214) 645-6353 (fax)

On May 1, 2019, at 3:22 PM, Whitley, Matthew J <mjw100 at pitt.edu<mailto:mjw100 at pitt.edu>> wrote:

Hello all,

We have collected electron diffraction data to approximately 1.8 Å on a 'small molecule' of roughly 1660 Da.  The space group (P 43 21 2) and unit cell parameters determined during data reduction match the known, published values, and our data are roughly 80% complete in all resolution shells from 17 - 1.8 Å.  We would like to solve this structure by molecular replacement in Phaser, but are having a bit of difficulty doing so.

Our problems all seem to be related to specifying the composition of the target molecule for Phaser.  Via the phenix GUI, we can only specify the target composition as either protein or nucleic acid, when in fact the target is neither.  The chemical composition of the target is C72 H85 N19 O18 S5.  Is there a way to feed this chemical composition to Phaser and to get it to understand that the target is neither protein nor nucleic acid?  Furthermore, according to our reading of the Phaser documentation, specifying "protein" leads to an assumed solvent content of 50%, which is likely to be a substantial overestimation for this small molecule crystal.  We have also run into the problem of Phaser complaining that the target molecule will not fit into the given unit cell, which we think is due to the assumption of 50% solvent content.

We would be thankful for whatever advice you may have on using Phaser with non-protein, non-nucleic acid molecules.


Matthew J. Whitley, Ph.D.
Research Instructor
W. Furey Lab
Department of Pharmacology & Chemical Biology
University of Pittsburgh School of Medicine
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