Re: [ccp4bb] disordered helix
This looks to me like a good attempt for GraphEnt. Give it a shot and you might be positively surprised. Jürgen Sent from my iPad On May 13, 2013, at 21:26, "Dale Tronrud" wrote: >Sometimes a floppy bit of a protein is even more floppy in a > particular crystal form. Your maps do not appear to support your > model of a helix in this location. I would not build it unless > maps based on later refinement show something reasonable in the > omit map. (Of course if you leave out the helix, all your maps > will be omit maps.) > >It is quite common to submit models to the PDB that do not > contain all of the amino acids expected based on the sequence. > If you can't see where the chain goes you certainly can't be > expected to build it. > > Dale Tronrud > > On 05/13/2013 04:23 AM, atul kumar wrote: >> I have attached the map and omit map(after deleting helix) images. >> >> 2Fo-Fc(1 sigma) >> >> Fo-Fc(3sigma) >> >> On 5/13/13, Eleanor Dodson wrote: >>> Hard to say without seeing the maps and experimenting. My first check would >>> be to set the NTD occupancies to 0.0 - refine the CTD alone, then look at >>> the maps in COOT. >>> >>> Or maybe let an automatic modelling building program such as Buccaneer try >>> to rebuild the NTD section, with starting phases from the CTD. >>> >>> Eleanor >>> >>> >>> >>> >>> On 13 May 2013 09:04, atul kumar wrote: >>> Dear all, I have solved the structure of my protein by molecular replacement at 2.9A, with Rfactor and Rfree 18 and 22 respectively. Overall everything seems fine, its a two domain protein NTD and CTD, the NTD have high average B factor compared to CTD. A helix of NTD seems to be disordered, I tried different geometric weights but the refined structure does not seem to follow proper geometry for this helix. The B-factor of this helix is very high compared to overall B factor for NTD and omit map shows only some partial density in this region( off course not conclusive). All the homologous structure have helix in this region although with high B-factor. Should I submit the current pdb or need more refinement? thanks and regards Atul Kumar >>>
Re: [ccp4bb] disordered helix
Sometimes a floppy bit of a protein is even more floppy in a particular crystal form. Your maps do not appear to support your model of a helix in this location. I would not build it unless maps based on later refinement show something reasonable in the omit map. (Of course if you leave out the helix, all your maps will be omit maps.) It is quite common to submit models to the PDB that do not contain all of the amino acids expected based on the sequence. If you can't see where the chain goes you certainly can't be expected to build it. Dale Tronrud On 05/13/2013 04:23 AM, atul kumar wrote: I have attached the map and omit map(after deleting helix) images. 2Fo-Fc(1 sigma) Fo-Fc(3sigma) On 5/13/13, Eleanor Dodson wrote: Hard to say without seeing the maps and experimenting. My first check would be to set the NTD occupancies to 0.0 - refine the CTD alone, then look at the maps in COOT. Or maybe let an automatic modelling building program such as Buccaneer try to rebuild the NTD section, with starting phases from the CTD. Eleanor On 13 May 2013 09:04, atul kumar wrote: Dear all, I have solved the structure of my protein by molecular replacement at 2.9A, with Rfactor and Rfree 18 and 22 respectively. Overall everything seems fine, its a two domain protein NTD and CTD, the NTD have high average B factor compared to CTD. A helix of NTD seems to be disordered, I tried different geometric weights but the refined structure does not seem to follow proper geometry for this helix. The B-factor of this helix is very high compared to overall B factor for NTD and omit map shows only some partial density in this region( off course not conclusive). All the homologous structure have helix in this region although with high B-factor. Should I submit the current pdb or need more refinement? thanks and regards Atul Kumar
Re: [ccp4bb] disordered helix
Hard to say without seeing the maps and experimenting. My first check would be to set the NTD occupancies to 0.0 - refine the CTD alone, then look at the maps in COOT. Or maybe let an automatic modelling building program such as Buccaneer try to rebuild the NTD section, with starting phases from the CTD. Eleanor On 13 May 2013 09:04, atul kumar wrote: > Dear all, > > I have solved the structure of my protein by molecular replacement at > 2.9A, with Rfactor and Rfree 18 and 22 respectively. Overall everything > seems fine, its a two domain protein NTD and CTD, the NTD have high average > B factor compared to CTD. A helix of NTD seems to be disordered, I tried > different geometric weights but the refined structure does not seem to > follow proper geometry for this helix. The B-factor of this helix is very > high compared to overall B factor for NTD and omit map shows only some > partial density in this region( off course not conclusive). All the > homologous structure have helix in this region although with high B-factor. > Should I submit the current pdb or need more refinement? > > thanks and regards > > Atul Kumar >
[ccp4bb] disordered helix
Dear all, I have solved the structure of my protein by molecular replacement at 2.9A, with Rfactor and Rfree 18 and 22 respectively. Overall everything seems fine, its a two domain protein NTD and CTD, the NTD have high average B factor compared to CTD. A helix of NTD seems to be disordered, I tried different geometric weights but the refined structure does not seem to follow proper geometry for this helix. The B-factor of this helix is very high compared to overall B factor for NTD and omit map shows only some partial density in this region( off course not conclusive). All the homologous structure have helix in this region although with high B-factor. Should I submit the current pdb or need more refinement? thanks and regards Atul Kumar
