[ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
Covalent modification?? Bias in 2fo-fc map? Can you show us a pic of offending density? Dave On 28/12/2007, Brenda Patterson [EMAIL PROTECTED] wrote: Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
What's the resolution? At low res it is possible to miss a subtle movement of e.g. some sidechains which are being replaced by the ligand. What quality parameters did the MR have? Can you omit the entire ligand binding site, refine, and re-generate the map - what does it look like after that? A picture would help! Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Brenda Patterson Sent: Friday, December 28, 2007 10:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure? Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
There is another possibility that your ligand is not fully occupied, if the binding site of protein endures an apparent change when bound by ligand. Lijun On Dec 28, 2007, at 7:55 AM, Brenda Patterson wrote: Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
On Fri, 28 Dec 2007 15:55:39 + Brenda Patterson [EMAIL PROTECTED] wrote: Hello, I am fairly new to this lark No problem. With a name like Patterson, your future is guaranteed (unless of course you see everything in the world with intensity but no phase). I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. ... how to proceed? The best thing to do at this point is to refine your structure while omitting the residues involved in the potential steric clash. The ligand may bind by induced fit -- i.e., changing the conformation at the binding site from that of the original structure. When you do that, the density that comes back will be less biased, and the answer to how it fits together may be apparent at that point.
