Dear Leif,

thanks for your feedback. The neutron data is to 90% complete. Yes, you are absolutely right. This is why in the first place I have refined the structure against neutron data only until convergence. It's just that we are very much interested in the water structure and here the addition of the X-ray data helps to orient waters correctly. The results agree astonishingly well with chemical intuition which is sometimes not the case when using only neutron data even though the resolution is comparably high. Waters simply have too many degrees of freedom and here the knowledge of the precise oxygen position helps a lot during modelling. Ultimately, we would like to deposit both, the pure neutron and the XN structure.

Regards,
Johannes


Am 14.10.2016 um 15:11 schrieb Leif Hanson:
Dear Johannes,
What is your completeness in your neutron data? I think at some point we need to stop hiding behind a joint refinement and use only the neutron data, especially with this level of resolution. I like your idea of fixing the ADP ratio. The more scientifically interesting question in this case is the exchange and not the B-factors. If you are really bothered by your X+N H/D coordinate and occupancy results, and your completeness is near 90% or higher, the more conservative result is to refine with SHELX.
Best wishes,
Leif Hanson

On Fri, Oct 14, 2016 at 5:45 AM, Johannes Schiebel <[email protected]> wrote:
Dear Tim,

thank you very much for your reply! I agree that it will be very difficult to get reasonable values for both, occupancy and ADPs, at usual neutron diffraction resolutions of around 2 A. However, we are talking about neutron diffraction data to 1.4 A and X-ray diffraction data to 0.9 A. So, we have a lot of data. I should have mentioned this right away, sorry. Do you think that in such a rare case it might be possible to get reasonable values?

Also, I like your idea to group H/D sites by expected exchange values. However, from the high-quality data we have, it is obvious that in a lot of cases the exchange rate is not really easy to predict by chemical intuition alone. There are sites where you clearly would expect at least a partial exchange but yet you observe a strong negative peak in the neutron scattering length density indicating the presence of an almost non-exchanged hydrogen . Wouldn't it also be possible to fix the ADP ratio between the H/D atoms and the atom to which they are attached to a chemically likely value between 1.0 and 1.5 and then refine only the occupancy? To me auch an approach seems less prone to errors introduced into the model by the crystallographer's expectations.

Best wishes,
Johannes



Am 13.10.2016 um 17:25 schrieb Tim Gruene:
Dear Johannes,

I would recommend not to refine the occupancy of individual H/D pairs, unless 
you have high resolution and other evidence for the resulting values. 
Occupancy and ADP-values are very strongly correlated, and the correlation 
becomes higher the worse your resolution. And neutron data often have 
resolution of 2A or worse.

You could group atoms together where you expect similar exchange ratios (based 
on chemical intuition) and refine one ratio per group. You can find a more 
detailed explanation in https://doi.org/10.1107/S1600576713027659

That article also recommends to treat X-ray data as additional information by 
means of geometry restraints to avoid the complications you get with joint 
refinement. The main effect of joint refinement are prettier maps <flame> and 
you may need to decide whether you want to focus on science or on art 
</flame>. This way we refined the structure also has the side effect to 
constrain H and D to the same location, although, admittedly, the coordinate 
difference in the structure you quote is probably negligible.

Best,
Tim


On Thursday, October 13, 2016 05:06:36 PM Johannes Schiebel wrote:

Hi everyone,

I am currently working on an X-ray/neutron (XN) joint refinement using
phenix.refine. As it should be, H/D coordinates and ADPs at exchangable
sites are refined to equal values when using Phenix version 1.10.1-2155
and neutron data only. This is also stated in the paper describing the
development of the method (Afonine et al. (2010) Joint X-ray and neutron
refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 66,
1153-1163) as the default behavior: "Currently, phenix.refine maintains
the H and D atoms at coinciding positions and constrains their ADPs to
be equal to each other". However, when switching to XN-refinement using
the same Phenix version, H and D atoms refine to different coordinates
and ADPs, which should not be the case as it leads to unrealistic
artifacts as can be seen from the deposited PDB 3X2P:

ATOM    186  H  AALA A  13       3.486 -18.200 -14.123  0.38
14.54           H
ATOM    187  D  BALA A  13       3.488 -18.195 -14.111  0.62
38.07           D

In this example, the D-occupancy is likely overestimated, while the
H-occupancy is underestimated because the ADPs refine to very different
values, which is chemically not reasonable.

Hence my question: How can I treat my data in a way that ADPs and
coordinates refine to the same values at exchangeable H/D sites also for
XN-refinement? Is there a specific keyword I am currently overlooking or
do I have to use another Phenix version?

I would be really glad to receive your feedback. Thanks in advance!

Kind regards,
Johannes

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