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I often say this, but check the anomalous difference Fourier. You don't say what resolution your data reaches to, or what wavelength the data is collected at, but if the model is well refined you often can see anomalous peaks for Ss, and they give you a relative scale for any anomalous feature which corresponds to that site. Eleanor Dodson On 22 June 2015 at 19:15, Roger Rowlett <[log in to unmask]> wrote: > I agree...one possibility is a M-His(2)-Lys-(OH2) site. Possible metal > ions would include Zn(II), although Lys is a relatively rare ligand in > zinc-metalloenzyme sites. > > Cheers, > > _______________________________________ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: [log in to unmask] > > > On 6/22/2015 11:20 AM, Keller, Jacob wrote: > >> Looks to me like a metal binding site with those histidines, perhaps--any >> chance of that? That might also explain the weird geometry issues. >> >> JPK >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of >> Dale Tronrud >> Sent: Monday, June 22, 2015 11:17 AM >> To: [log in to unmask] >> Subject: Re: [ccp4bb] distorted phosphate molecule geometry after >> refinement >> >> It is possible that your PO4 has its atoms labeled with the wrong >> chirality. Yes, I know that PO4 is not chiral when you ignore hydrogen >> atoms and single/double bonds but adding labels creates an unnatural >> chriality. Try your refinement again after switching the labels on two >> oxygen atoms. >> >> Dale Tronrud >> >> On 6/22/2015 7:48 AM, ansuman biswas wrote: >> >>> Dear CCP4 users, >>> >>> I am working on a protein from a hyperthermophilic archaeon. >>> >>> I have collected mutliple X-Ray datasets, both from home source and >>> synchrotron and always found a clear density for tetrahedral geometry, >>> co-ordinated by two histidines and one lysine. >>> >>> I tried fitting phosphate there, but its geometry always gets >>> distorted after each refinement cycle (Refmac 5.8.0073). Also I found >>> some short contacts between the coordinated residues and phosphate >>> which were very difficult to remove. >>> >>> I am attaching a figure with the density and phosphate. >>> >>> Kindly suggest - >>> 1. if this may be a possible modification of any of the associated >>> residues, and the code of the modified residue to be used. >>> >>> 2. If the ligand requires separate restraints during refinement, I am >>> using the "restrained refinement" option available at the top of the >>> GUI for refmac. >>> >>> Thanking you, >>> yours sincerely, >>> Ansuman Biswas, >>> PhD student, >>> Dept. of Physics, >>> IISc >>> >>>