Dear Catherine,
Regardless with program you use for refinement, I would recommend to use
dictionary from the monomer library for HEM from the very latest CCP4
version (9.0.010). All the metal-containing monomers were recently
updated and fixed with the help of the MetalCoord program. You can also
get the library directly from GitHub:
https://github.com/MonomerLibrary/monomers
However, this will most likely not solve your particular problem with
the peak in diff. density. Anyway, the refinement should be more stable
and reported geometry outliers more relevant.
Best regards,
Martin
On 05/09/2025 13:50, Catherine Back wrote:
Hi All,
Many thanks for all your suggestions. I've had some direct replies as
well as all the ones from the BB.
*
The occupancies were definitely 1.0
*
I'll refine anisotropically from now on.
*
The Bfactors for two of the Fe-atoms were abnormally high, which
contributed to the density. I've altered them and they've gone
back down to similar levels to the surrounding atoms.
*
The collection wavelength was 0.976 Å.
*
I was using Phenix Refine, though I tried Refmac first.
There is still a little positive density in the area of the Fe, but
the structure is well refined, so possibly this is just amplifying any
tiny errors?
Cheers,
Catherine
Dr Catherine R. Back (she/her)
Senior Post-doctoral Research Associate
School of Biochemistry
University of Bristol
UK
------------------------------------------------------------------------
*From:* CCP4 bulletin board <[email protected]> on behalf of Jon
Cooper <[email protected]>
*Sent:* 05 September 2025 13:17
*To:* [email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Green density over Fe in heme
Treating the iron (Fe) as fluorine (F) is roughly equivalent having
the iron occupancy at (9/26) or 0.34 approx ;-0
Best wishes, Jon Cooper.
[email protected]
Sent from Proton Mail Android
-------- Original Message --------
On 05/09/2025 13:03, Garib Murshudov
<[email protected]> wrote:
In my experience there could be several reasons for green
densities around metal atoms:
1) occupancy. In this case it is unlikely to be a problem
2) effect of f’ if it is strong. It is visible at higher
resolution more than at low resolutions.
3) B vallues, isotropic or anisotropic. B value of the metal
should be very similar to that of the well defined surrounding atoms
4) Multiple positions due to mixtures of charges and coordination
geometries
Regards
Garib
On 5 Sep 2025, at 12:47, Ezra Peisach
<[email protected]> wrote:
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--
I know you mentioned that this was not an anomalous map, but what
at wavelength were your data collected at? Fe has a significant
f" at CuKalpha (1.54..) wavelength.
On 9/5/25 7:37 AM, Jon Cooper wrote:
I would check the iron occupancy in case it is less than 1.0 and
that your Fe has the left-shift in the PDB file otherwise it
might be treated as a fluorine? Good old pdb format.
Best wishes, Jon Cooper.
[email protected] <mailto:[email protected]>
Sent from Proton Mail Android
-------- Original Message --------
On 05/09/2025 10:40, Catherine
Back<[email protected]>
<mailto:[email protected]>wrote:
Good morning,
I am currently solving a structure containing four heme b
molecules (res 1.7 Å), each coordinated by two histidines.
The refinement is looking good, but the output from
refinement has marked the Fe ions of each heme with positive
density (green) in the FoFc difference map - see image. Any
ideas why? I used the Monomer Library in Coot to add hemes
('HEM') in. Is it something to do with the oxidation state
of the Fe? And if so, is there anything I can do about it?
Best wishes,
Catherine
Dr Catherine R. Back (she/her)
Senior Post-doctoral Research Associate
School of Biochemistry
University of Bristol
UK
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