Oh, had assumed it was the S- absolute configuration ... TriNgo? J ------------------------------ Dr Judith Murray-Rust Structural Biology Laboratory Cancer Research UK.
> -----Original Message----- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On > Behalf Of Roger Rowlett > Sent: 27 July 2009 13:35 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Problem with different map when ligand > refinement > > Is the correct ligand HOCH2CH(CH3)C(O)SCH3? The ligand > depicted in the density map is HOCH2CH(CH3)C(O)OCH3. > > Cheers, Roger Rowlett > > > Ngo Duc Tri wrote: > > Dear ccp4 experts, > I am trying to solve the structure of one esterase with > its substrate. The structure was solved by MR to the > resolution 2.2 A. In the active site, I can see clearly the > different density map of the substrate (S- methyl hydroxy > isobutyrate). After puting the substrate into that density > map, I use Refmac to run restrain refinement at 0.1 weighting term. > Even though the substrate fits to the different map > very well, a big different map appears at one end of the > substrate after Refmac refinement. I attach the image so that > it's easy to see the problem. > I tried to put water or Na (because the crystallization > contains: 1M sodium citrate, 100mM Na Cacodylate, 20% > glycerol) but it didn't work. > I tried to use CNS instead of Refmac, however the > result is worse since the R-free is increased and the > different map is still there. Because I am new with CNS so I > don't know which parameters I should adjust. > Do you have any suggestion to solve this problem? Thank > you very much for all of your helpful advice! > > My best regards, > TriNgo, > PhD student, > Sungkyunkwan University, Korea > > ________________________________ > > > > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
