Dear all, I have a question regarding the heme c geometry restraint. I am aware that heme c could undergo distortion when bound to protein, but I am not sure at what resolution I could claim such distortion (such as ruffling/bending/doming). I have a map at 3.6 A resolution and whenever I did the refinement in phenix with real space refinement, some of the hemes are distorted and I am wondering if it is justified to leave it that way or do I have to impose the flat plane geometry. If so, how should I proceed to impose such geometry? Thank you in advance! Best, Yangqi
Yangqi
@ 3.6Å resolution, you would almost certainly not have enough information
to suggest anything but planar geometry. I'm happy to take a look if you
send me the model and restraints directly.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Sun, Jul 19, 2020 at 5:24 PM Yangqi Gu
Dear all, I have a question regarding the heme c geometry restraint. I am aware that heme c could undergo distortion when bound to protein, but I am not sure at what resolution I could claim such distortion (such as ruffling/bending/doming). I have a map at 3.6 A resolution and whenever I did the refinement in phenix with real space refinement, some of the hemes are distorted and I am wondering if it is justified to leave it that way or do I have to impose the flat plane geometry. If so, how should I proceed to impose such geometry? Thank you in advance! Best, Yangqi _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
On 20/07/2020 01:20, Yangqi Gu wrote:
Dear all, I have a question regarding the heme c geometry restraint. I am aware that heme c could undergo distortion when bound to protein, but I am not sure at what resolution I could claim such distortion (such as ruffling/bending/doming). I have a map at 3.6 A resolution and whenever I did the refinement in phenix with real space refinement, some of the hemes are distorted and I am wondering if it is justified to leave it that way or do I have to impose the flat plane geometry. If so, how should I proceed to impose such geometry? Thank you in advance!
During my PhD I was fortunate enough to sit down at the graphics (a E&S PS390) with Michael Rossmann to show him my current Hb model. He expressed some scepticism about the way I had modelled the heme. "Make it flat and show me the difference map" he said. The point being that if it truly was buckled then we'd see several significant difference map peaks (at say 3.0 rmsd) around the pyrroles (not the Iron atom) consistent with the buckled model. Paul.
Dear Paul, Nice story: constrain and watch whether the data complain - otherwise "Where freedom is given, liberties will be taken". And did you see significant difference density after enforcing flatness? With best wishes, Gerard. -- On Tue, Jul 21, 2020 at 07:13:49PM +0100, Paul Emsley wrote:
On 20/07/2020 01:20, Yangqi Gu wrote:
Dear all, I have a question regarding the heme c geometry restraint. I am aware that heme c could undergo distortion when bound to protein, but I am not sure at what resolution I could claim such distortion (such as ruffling/bending/doming). I have a map at 3.6 A resolution and whenever I did the refinement in phenix with real space refinement, some of the hemes are distorted and I am wondering if it is justified to leave it that way or do I have to impose the flat plane geometry. If so, how should I proceed to impose such geometry? Thank you in advance!
During my PhD I was fortunate enough to sit down at the graphics (a E&S PS390) with Michael Rossmann to show him my current Hb model. He expressed some scepticism about the way I had modelled the heme. "Make it flat and show me the difference map" he said. The point being that if it truly was buckled then we'd see several significant difference map peaks (at say 3.0 rmsd) around the pyrroles (not the Iron atom) consistent with the buckled model.
Paul.
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participants (4)
-
Gerard Bricogne -
Nigel Moriarty -
Paul Emsley -
Yangqi Gu