Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit
As an update, this approach did not work in Refmac, but as Pavel suggested it worked fine with phenix.refine. --paul On 08/23/2013 11:51 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Paul, have you actually tried using the 'alternate location indicator' with two different residues? I would not be surprised if that would work with refmac. Best, Tim On 08/23/2013 05:39 PM, Paul Paukstelis wrote: Greetings, We have been working on a few DNA crystals in which the asymmetric unit contains a stoichiometric (or nearly so) mixture of two similar but distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but for a few of these there are some hints from the density for two different bases at the same position. I'm curious what the best way to approach refinement would be in this case. Alternate conformation doesn't really work since the residues have different nucleobases. Having two complete chains with 0.5 occupancy is overkill since there are only 2 (or 4) positions in which the sequence differs. I tried just adding a second chain for the varying residues at 0.5 occupancy and adding link records to the original chain, however this doesn't seem to respect geometry of the phosphodiester for the flanking residues. I would appreciate suggestions or any examples in the PDB that might set me in the right direction. --paul - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSF4T7UxlJ7aRr7hoRAtC9AKCeIcRnKeCrsW4/QY7ad5xooRw73wCgvEpw ite155+O8JylmpSS454gYXM= =3lH/ -END PGP SIGNATURE-
Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit
Hi Paul, I would have them both in PDB file with different non-blanc altLocs and arbitrary starting occupancies and that will work in refinement (in phenix.refine for sure, can't tell for other programs). Pavel On Fri, Aug 23, 2013 at 8:39 AM, Paul Paukstelis wrote: > Greetings, > > We have been working on a few DNA crystals in which the asymmetric unit > contains a stoichiometric (or nearly so) mixture of two similar but > distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but > for a few of these there are some hints from the density for two different > bases at the same position. I'm curious what the best way to approach > refinement would be in this case. Alternate conformation doesn't really > work since the residues have different nucleobases. Having two complete > chains with 0.5 occupancy is overkill since there are only 2 (or 4) > positions in which the sequence differs. I tried just adding a second chain > for the varying residues at 0.5 occupancy and adding link records to the > original chain, however this doesn't seem to respect geometry of the > phosphodiester for the flanking residues. I would appreciate suggestions or > any examples in the PDB that might set me in the right direction. > > --paul >
Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Paul, have you actually tried using the 'alternate location indicator' with two different residues? I would not be surprised if that would work with refmac. Best, Tim On 08/23/2013 05:39 PM, Paul Paukstelis wrote: > Greetings, > > We have been working on a few DNA crystals in which the asymmetric > unit contains a stoichiometric (or nearly so) mixture of two > similar but distinct oligonucleotides. The resolution is medium to > low (2.7-2.8) but for a few of these there are some hints from the > density for two different bases at the same position. I'm curious > what the best way to approach refinement would be in this case. > Alternate conformation doesn't really work since the residues have > different nucleobases. Having two complete chains with 0.5 > occupancy is overkill since there are only 2 (or 4) positions in > which the sequence differs. I tried just adding a second chain for > the varying residues at 0.5 occupancy and adding link records to > the original chain, however this doesn't seem to respect geometry > of the phosphodiester for the flanking residues. I would appreciate > suggestions or any examples in the PDB that might set me in the > right direction. > > --paul > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSF4T7UxlJ7aRr7hoRAtC9AKCeIcRnKeCrsW4/QY7ad5xooRw73wCgvEpw ite155+O8JylmpSS454gYXM= =3lH/ -END PGP SIGNATURE-
[ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit
Greetings, We have been working on a few DNA crystals in which the asymmetric unit contains a stoichiometric (or nearly so) mixture of two similar but distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but for a few of these there are some hints from the density for two different bases at the same position. I'm curious what the best way to approach refinement would be in this case. Alternate conformation doesn't really work since the residues have different nucleobases. Having two complete chains with 0.5 occupancy is overkill since there are only 2 (or 4) positions in which the sequence differs. I tried just adding a second chain for the varying residues at 0.5 occupancy and adding link records to the original chain, however this doesn't seem to respect geometry of the phosphodiester for the flanking residues. I would appreciate suggestions or any examples in the PDB that might set me in the right direction. --paul
