For small ion soaking for phasing purposes, partial occupancy is not a problem. For example, a few 1/2 occupied Iodines still can phase quite well. 1/2 a C is only 3 electrons, not that great. Add in higher displacement, and odds are that the ligand interpretation will become difficult. Particularly when the binding constants are poor, one will out of principle never reach full occupancy, which further exacerbates the weak density problem. Patience is definitely a virtue here.
BR -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Friday, June 27, 2014 3:07 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels ....And yet halides--even iodide--permeate those same lysozyme crystals and others entirely in <30--60 sec. JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp Sent: Friday, June 27, 2014 9:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Just a remark: diffusion is a slow and random-walk process. Particularly large molecules in viscous media (PEG anybody?) move (diffuse) slowly in solution. To simply extrapolate from the fact that the ligand is smaller than the solvent channels to the odds of the presence of a ligand is a risky proposition. Positive omit difference density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. The little movie below shows how slowly even a small aromatic dye molecule soaks into a crystal. Total time 10 hrs. http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv The literally hundreds of empty ligand structures collected in Twilight attest to that fact. http://journals.iucr.org/d/issues/2013/02/00/issconts.html Best, BR Science is a way of trying not to fool yourself: The first principle is that you must not fool yourself - and you are the easiest person to fool. R. Feynman, 1974 -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz Shaanan Sent: Friday, June 27, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Hi, I'm not aware of a program with an option to display channels in crystals but if you use any of the currently available molecular display program and ask to display symmetry-related molecules + adjacent unit cells, it should give you a good enough idea of the spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza Khayat [rkha...@ccny.cuny.edu] Sent: Friday, June 27, 2014 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org =
