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Another suggestion: The atom with a low B-factor might be the S of the sulphonate group in HEPES or MES, as in buffers. Good Luck. Pierre ************************************************************************ ******* Pierre Rizkallah, Daresbury Laboratory, Warrington, Cheshire WA4 4AD, U.K. Phone: (+)44 1925 603808 Fax: (+)44 1925 603124 e-mail: [EMAIL PROTECTED] html: http://www.srs.ac.uk/px/pjr/ -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Corn Sent: 20 April 2006 17:40 To: Segura Pena, Dario Cc: [email protected] Subject: Re: [ccp4bb]: Very low B factor after Refmac *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi Dario, I would suspect that the MPD is not actually MPD, but instead something with a similar makeup/geometry that contains an electron-dense atom, such as phosphate. For example, MPD looks like this C C \ / C*-C-C (C2 marked by C*) / \ \ C O O and pyrophosphate looks like this O O O \ \ / P*-o-P / \ \ O O O Not that I'm saying you have pyrophosphate in there (at 1.5A, you'd probably be able to see that extra oxygen). But you should consider all of the other things enzyme may have either grabbed out of the drop or brought along from the cell. Jacob Segura Pena, Dario wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Dear all, > > Recently I obtained protein crystal that grew in 60 % MPD. The crystal > diffracts very well to 1.5 Ǻ. It seems that an MPD molecule is in the > active center of the enzyme, however the atom C2 of the MPD molecule has a > B factor of 2 after several cycles of refinement with Refmac. > Does anybody have any idea why the there is such a low B factor for this > atom?.The electron density for the region corresponding to the atom C2 of > the MPD molecule is visible at 5 sigma level in a 2fo-fc map while at 3 > sigma level there is not electron density for the rest of the molecule. > > I will appreciate any ideas or suggestions. > > Sincerely, > Dario > -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology [EMAIL PROTECTED] phone: 510-643-8893 fax: 510-643-9290
