Dear Pavel. Thank you very much for your answer and explanations. Actually, in the first place I already refined against neutron data (without X-ray) until convergence and the results are quite good. However, water orientations (in which we are particularly interested) are not easily discernible in the maps since the knowledge about water oxygen positions from the X-ray data are not explicitly implemented during refinement. Hence, we collected room-temperature X-ray data from a deuterated crystal grown in the same drop as the crystal used for neutron diffraction experiments. With the combined XN-data, it is astonishing how the R-free of both X-ray and neutron data drop significantly (by 2% for the neutron part) and how well the data agree. To account for the longer X-D/H bond lengths in nuclear density maps, we used the respective restraints for neutron data (Settings --> Advanced --> Model interpretation --> Use the nuclear distances for X-H/D). Overall, I would really like to use the XN-refinement approach to improve the model in particular with respect to its water structure. Ultimately, we will anyhow deposit the neutron, X-ray and joint XN structures. Is it not possible at all to achieve coinciding coordinates and identical ADPs when using X and N at the same time? The only alternative that I have not already used and would further improve the water structure in the model would be what you describe under 3. From what I read about it, however, it will be difficult to generate restraints also for water oxygens for which it would be particularly important in our case. Or is this possible in addition to the dihedral restraints for the protein? Thanks a lot! Best, Johannes Am 14.10.2016 um 16:09 schrieb Pavel Afonine:
Hi Johannes,
historically, in joint Xray+Neutron refinement first tried by Coppens et al (1981) in small molecule world and later (1982) by Wlodawer & Hendrickson in bio-macromolecules, and way later implemented in refinement tools such as nCNS (2009) and Phenix (2010), one single model is refined against two data sets, Xray and neutron.
The rationale to use two data sets, Xray and neutron, is to alleviate the seemingly poor data-to-parameters ratio because H and D are used explicitly in refinement using neutron data. This is all discussed in great details in that 6 years old paper:
https://www.phenix-online.org/papers/dz5209_reprint.pdf
Turns out with a proper data / restraints weight the problem of data-to-parameters amount is not as bad as it may appear, since by varying the weight one can dose the amount of a priori knowledge (restraints) as desired. This makes it possible to refine one model against X-ray or neutron data individually without problems.
Also, we know that X-H distances for X-ray and neutron are different (X-ray are shorter a tiny bit). We also know that both data sets may be collected at different temperatures (neutron at room, and X-ray at cryo), which means B factors are going to be different, some rotamers may be different, water structure may be slightly different, and so on. All in all we really do need to have two structures to maximize the use of available information. This is the new refinement paradigm that's being implemented in phenix.refine and will become available at some point.
The best you can do right now is:
1) Get the best possible refined X-ray structure (refined against x-ray data set alone); 2) Use refined x-ray structure as a starting point for neutron refinement (add H,D as appropriate - trivially done using phenix.ready_set or using Phenix GUI); 3) Refine structure from #2 against neutron data set alone. This will make sure H and D have identical coordinates and B. If really needed you can supply X-ray structure as a reference model - also trivially done from the phenix.refine GUI.
Let us know should you have questions or need help.
Pavel
On 10/13/16 23:06, 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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