Hi Pat I concur with George, we routinely refine together the group B factor and occupancy of our ligands and frequently see significant deviations of the group occupancy from the starting value even if it is highly correlated with the group B factor (the significance test takes account of the correlation), sometimes at 2.8 Ang, but rather easily detectable at 2 Ang. This often eliminates negative difference density, particularly at the heavier atoms such as S, Cl, Br (of course this could also be explicable by inducement of disorder by radiation damage as opposed to the ligand binding with partial occupancy on soaking or co-crystallisation). Whenever I see a significant difference (say > 10 Ang.^2) between the average B factor of the ligand and the average B factor of the protein atoms in the binding site I suspect that partial occupancy of the ligand is the true explanation.
There is in fact no reason why the occupancy and B factor should be completely correlated, unless of course the data errors are large and/or the resolution is very low and/or the group only makes a small contribution to the total scattering, in which the errors will dominate and the results will not be significant. This is because increasing the B factor of an atom or group of course makes the density broader and lower but does not change the integral of the density (i.e. the number of electrons scattering), whereas changing the occupancy clearly does change the number of electrons (in fact proportionally). Hence the effects of changing the B factor and occupancy are quite different. Cheers -- Ian PS I wasn't your referee either! > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of George M. Sheldrick > Sent: 31 May 2009 17:20 > To: Patrick Loll > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] coupling between occupancy and b-values in > refinement > > Dear Pat, > > You don't say how large your ligand is, but if the occupancy is > refined as a single parameter so that all the atoms in the ligand > are constrained to have the same occupancy, it should be rather > well-defined and not highly correlated with the B-values. By > the way, I was not your referee! > > Best wishes, George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Sun, 31 May 2009, Patrick Loll wrote: > > > Hi all, > > > > I'm looking for a reference to bolster my response to a referee, in > which I > > defend my decision not to refine the occupancy of a ligand in structure > > refined at around 2 A resolution (note the ligand binding slte lies on a > > two-fold crystallographic axis, so the maximum occupancy is 0.5) > > > > I recall reading a paper a LONG time ago (decades) in which someone > described > > some careful refinement experiments, and concluded that the correlation > > between occupancy and B-value is so strong that it simply makes no sense > to > > "independently" refine both parameters (at least for light atoms, and in > the > > absence of super high resolution data). > > > > Alas, all that I recall is this take-home message. I have no idea of > where the > > paper appeared, or the names of the authors (or indeed, if I'm even > > remembering the paper's message correctly). I've tried trolling through > Acta, > > without success. Does anyone have a better idea of where I might find > this > > paper, or one espousing a similar message? > > > > Thanks, > > > > Pat > > > > > > ------------------------------------------------------------------------ > ------------- > > Patrick J. Loll, Ph. D. Professor of > > Biochemistry & Molecular Biology > > Director, Biochemistry Graduate Program > > Drexel University College of Medicine > > Room 10-102 New College Building > > 245 N. 15th St., Mailstop 497 > > Philadelphia, PA 19102-1192 USA > > > > (215) 762-7706 > > pat.l...@drexel.edu > > > > > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
