Dear Murpholino Unfortunately no rule of thumb has been established, although I have only seen contraction once and have seen expansion for very many proteins. Seems to depend critically on the particular crystal (and probably its density of stacking imperfections/dislocations) and even crystals of the same protein from the same growth drop do not behave in the same way, as shown in 2 systematic studies of this phenomenon: Ravelli et al., JSR (2002) 9 Murray and Garman, JSR (2002) 9, 347-354. Best wishes Elspeth
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward Snell Sent: 07 March 2019 20:56 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] change in unit cell volume Hi Murpholino, I’ve looked at this with respect to metals in the protein and found that it was very informative to compare fractional coordinates which compensate for the volume expansion. When that is done, some apparent motions may be simply due to unit cell expansion (waters, metals, ligands etc.), while others can be very specific and produce structural non-isomorphism. I suspect the chemical damage has much more of an impact. Owen, Rudino-Pinera and Garman (PNAS, 2006) recommend an absolute maximum dose of 30 MGy. I’ve not compared cell expansion as a function of dose for a large sample of proteins but in a recent study (conveniently just heading for publication) I have seen a linear ~0.3% expansion per MGy which gives ~1% at 30 MGy. I don’t know if it’s the same for other proteins but I seem to remember a study or two on this and fully expect the authors to give me grief for forgetting them at the moment! Unit cell decreases could possibly be an impact of specific damage to crystallization contacts, off center crystals (if it’s within a data set), detector shifts or energy changes (both unlikely). I’ve not heard of a unit cell decrease being driven by damage but that’s not to say that it doesn’t happen. Best, Eddie PS. Shameless plug –- http://getacrystal.com Edward Snell Ph.D. Biological Small Angle Scattering Theory and Practice, Eaton E. Lattman, Thomas D. Grant, and Edward H. Snell. Available through all good bookshops, or direct from Oxford University Press Director of the NSF BioXFEL Science and Technology Center President and CEO Hauptman-Woodward Medical Research Institute BioInnovations Chaired Professorship, University at Buffalo, SUNY 700 Ellicott Street, Buffalo, NY 14203-1102 hwi.buffalo.edu Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esn...@hwi.buffalo.edu<mailto:esn...@hwi.buffalo.edu> Webpage: https://hwi.buffalo.edu/scientist-directory/snell/ [cid:image002.png@01D4D58B.E18F91C0] Heisenberg was probably here! From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Murpholino Peligro Sent: Thursday, March 7, 2019 3:33 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] change in unit cell volume Let's say I have a protein crystal from which I collected 30 datasets. If I plot the unit cell volume per dataset the volume rises. My question is: Is there a rule of thumb of some sort* to consider the initial/final datasets isomorphous still? * Something like if the unit cell volume changes more than 1% then the crystal is not isomorphous. My second question is: Meents already said that the unit cell volume expansion is a consequence of hydrogen gas building up inside the crystal. But...what if the unit cell volume decreases? Is there an explanation for that? Thank you very much. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
