Sorry to bring up an old thread. While tidying up my model before deposition, I noticed that in eLBOW, the HEM restraint has a charge of 0 for the Fe atom. Shouldn't this be +2 or +3? Usually Fe atom gets reduced by X-ray anyway. Or does this only matter for those doing molecular dynamics? On Tue, Mar 31, 2015 at 10:21 PM, Edward A. Berry wrote:

On 03/31/2015 02:12 PM, Pavel Afonine wrote: ~~~~~~~~~~~~~~~~

...

In fact, the C atom is covalently linked to the nearest Cys, so the

...

HEM side chain should be 'moved' into the density and the green blob shouldn't be there.

Is this link defined anywhere in restraints used in refinement?

Pavel

Here is an example of restraints for heme c. Values are from the high-resolution structure 1C75. Here residue 501 is the heme of course; and 37, 40, 41, and 160 are the C,C,H, and M in CxxCH---M heme c binding motif. I use HEC.cif for the heme parameters, but make sure the bond lengths in the vinyl groups are consistent with single bonds.

geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain D and resid 501 and name FE atom_selection_2 = chain D and resid 41 and name NE2 symmetry_operation = None distance_ideal = 1.99 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resid 501 and name FE atom_selection_2 = chain D and resid 160 and name SD symmetry_operation = None distance_ideal = 2.33 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resname CYS and resid 37 and name SG atom_selection_2 = chain D and resname HEC and resid 501 and name CAB symmetry_operation = None distance_ideal = 1.815 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resname CYS and resid 40 and name SG atom_selection_2 = chain D and resname HEC and resid 501 and name CAC symmetry_operation = None distance_ideal = 1.815 sigma = 0.1 slack = None }

...

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Hi Nigel I was referring to the partial charge in the restraint file, which IMHO should be translated to the model. I have a second problem - I'm using the cif file for refinement but the angles and bond lengths still get distorted. These are flagged as outliers in phenix.refine. Why is it not using the values that I input? My resolution is 3.8 A, but I still end up with positive density around all the hemes. In fact, the problems with hemes are the cause of a large majority of my outliers. I did a parallel refinement with and without the restraint file - it doesn't make any difference. Mohamed On Sat, May 23, 2015 at 4:47 PM, Nigel Moriarty wrote:

Mohamed

I'm not sure what you mean.

Firstly, I would hope you used the default restraints available in Phenix rather that generate restraints in eLBOW.

Secondly, are you talking about the formal charge in the model file or the partial charges in the restraints file.

Cheers

Nigel

--- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Fri, May 22, 2015 at 11:01 PM, mohamed noor wrote:

...

Sorry to bring up an old thread. While tidying up my model before deposition, I noticed that in eLBOW, the HEM restraint has a charge of 0 for the Fe atom. Shouldn't this be +2 or +3? Usually Fe atom gets reduced by X-ray anyway. Or does this only matter for those doing molecular dynamics?

On Tue, Mar 31, 2015 at 10:21 PM, Edward A. Berry wrote:

...

On 03/31/2015 02:12 PM, Pavel Afonine wrote: ~~~~~~~~~~~~~~~~

...

In fact, the C atom is covalently linked to the nearest Cys, so the

...

HEM side chain should be 'moved' into the density and the green blob shouldn't be there.

Is this link defined anywhere in restraints used in refinement?

Pavel

Here is an example of restraints for heme c. Values are from the high-resolution structure 1C75. Here residue 501 is the heme of course; and 37, 40, 41, and 160 are the C,C,H, and M in CxxCH---M heme c binding motif. I use HEC.cif for the heme parameters, but make sure the bond lengths in the vinyl groups are consistent with single bonds.

geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain D and resid 501 and name FE atom_selection_2 = chain D and resid 41 and name NE2 symmetry_operation = None distance_ideal = 1.99 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resid 501 and name FE atom_selection_2 = chain D and resid 160 and name SD symmetry_operation = None distance_ideal = 2.33 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resname CYS and resid 37 and name SG atom_selection_2 = chain D and resname HEC and resid 501 and name CAB symmetry_operation = None distance_ideal = 1.815 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resname CYS and resid 40 and name SG atom_selection_2 = chain D and resname HEC and resid 501 and name CAC symmetry_operation = None distance_ideal = 1.815 sigma = 0.1 slack = None }

...

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Dear mohamed noor, in X-ray refinement one electron this way or the other would not make much difference until you are working with data in the charge density region (below, say 0.6A). At normal resolution ranges you cannot distinguish really between N, C, O, so for Fe with three times as many electrons, +2 or +3 wouldn't have much effect. Best, Tim On Sat, May 23, 2015 at 07:01:01AM +0100, mohamed noor wrote:

Sorry to bring up an old thread. While tidying up my model before deposition, I noticed that in eLBOW, the HEM restraint has a charge of 0 for the Fe atom. Shouldn't this be +2 or +3? Usually Fe atom gets reduced by X-ray anyway. Or does this only matter for those doing molecular dynamics?

On Tue, Mar 31, 2015 at 10:21 PM, Edward A. Berry wrote:

...

On 03/31/2015 02:12 PM, Pavel Afonine wrote: ~~~~~~~~~~~~~~~~

...

In fact, the C atom is covalently linked to the nearest Cys, so the

...

HEM side chain should be 'moved' into the density and the green blob shouldn't be there.

Is this link defined anywhere in restraints used in refinement?

Pavel

Here is an example of restraints for heme c. Values are from the high-resolution structure 1C75. Here residue 501 is the heme of course; and 37, 40, 41, and 160 are the C,C,H, and M in CxxCH---M heme c binding motif. I use HEC.cif for the heme parameters, but make sure the bond lengths in the vinyl groups are consistent with single bonds.

geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain D and resid 501 and name FE atom_selection_2 = chain D and resid 41 and name NE2 symmetry_operation = None distance_ideal = 1.99 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resid 501 and name FE atom_selection_2 = chain D and resid 160 and name SD symmetry_operation = None distance_ideal = 2.33 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resname CYS and resid 37 and name SG atom_selection_2 = chain D and resname HEC and resid 501 and name CAB symmetry_operation = None distance_ideal = 1.815 sigma = 0.1 slack = None } bond { action = *add delete change atom_selection_1 = chain D and resname CYS and resid 40 and name SG atom_selection_2 = chain D and resname HEC and resid 501 and name CAC symmetry_operation = None distance_ideal = 1.815 sigma = 0.1 slack = None }

...

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A