Picture of electron density didn’t come through, but three planar fused rings sounds like a flavin - is your protein involved in redox reactions and is it coloured when concentrated ? The only four ring molecules that spring to mind are steroids, but these wouldn’t be all that flat and you would get a sense of the pucker of the rings at that resolution.
On 27 Nov 2016, at 10:34, CCP4BB automatic digest system <lists...@jiscmail.ac.uk<mailto:lists...@jiscmail.ac.uk>> wrote: There are 2 messages totaling 65823 lines in this issue. Topics in this special issue: 1. Problems finding the correct Cif file of a crystal structure 2. Density for an unknown ligand ---------------------------------------------------------------------- Date: Sun, 27 Nov 2016 10:09:48 +0000 From: Harry Powell <ha...@mrc-lmb.cam.ac.uk<mailto:ha...@mrc-lmb.cam.ac.uk>> Subject: Re: Problems finding the correct Cif file of a crystal structure Hi Cambridge Structural Database (CSD) should have only those small molecule structures that have at least one organic carbon - so it may have copper acetate (but which? There may be several...). For strictly inorganic structures you would need the Inorganic Crystal Structural Database (ICSD). Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 26 Nov 2016, at 22:23, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: There is a data bae - cambridge Structural Data Base with most crystal structures coordinates and measure data in it. if your university subscribes you should be able to acess it. Eleanor dodson On 26 November 2016 at 21:00, Bianca Valdes <bianca.valdes...@gmail.com<mailto:bianca.valdes...@gmail.com>> wrote: Hello! I'm currently a PhD student. I'm taking a crystallography class and for our final project the professor wants us to compare the theoretical cif file of Copper Acetate with the experimental one we are generating. I found a cif file but is very incomplete, do you guys now where I can find the complete and correct Cif file for Copper Acetate? Thanks a lot! Bianca ------------------------------ Date: Sun, 27 Nov 2016 18:33:34 +0800 From: Wei Liu <we...@me.com<mailto:we...@me.com>> Subject: Density for an unknown ligand Dear all, We have recently crystallized a recombinant protein produce from E. coli, and determined the structure at 1.9 Å. The asymmetric unit contains two protein monomers. Beyond our expectation, strong Fo - Fc density is present at a cleft of one subunit, but not in the other. Density maps are given in the snapshots attached to this email. We tried to model Tris or Bis-tris propane that were used as the purification and crystallization buffers, but apparently either of them poorly fitted in this density. The molecule that can be modeled here seems more likely to be a ligand comprising 3 or 4 rings with good planarity, however we did not add any additives in our crystallization trials. So we think it should be something from E. coli, which has high affinity to our protein. I wonder if anybody can figure out which molecule well fits to the electron density. Best wishes Wei Liu ------------------------------ End of CCP4BB Digest - 26 Nov 2016 to 27 Nov 2016 - Special issue (#2016-322) ***************************************************************************** -------------------------------------------------------------------------------- Laurence H. Pearl PhD FRS FMedSci Professor of Structural Biology and Head of School of Life Sciences University of Sussex, Brighton, BN1 9RH, UK Phone +44-(0)1273 876 544: PA +44-(0)1273 872 699 -------------------------------------------------------------------------------- "Live Modestly and do Serious Things .. " - Dorothy Crowfoot Hodgkin --------------------------------------------------------------------------------
