Dear Rafal, with such a small molecule, and if you really have 1.0A resolution, you should be able to solve the structure by direct methods with shelxt. By default, shelxt searches all space groups in the Laue group. The output will not be very practical to assign residue, etc. but at least it might give you a clue where the problem is.
Best regards, Tim On Thu, 30 Jul 2020 14:05:54 +0200 Rafal Dolot <rdo...@cbmm.lodz.pl> wrote: > Dear all, > > Thank you for the response. I will try to explain it more precisely. > > The molecule of interest is a duplex with 9 nt length, but is paired > on the length of eight bases, with overhangs at ends. Molecules form > a parallel strings across the crystal lattice, parallel to C-axis, > because of these stacked overhangs. The structure was solved by MR > using Molrep. Trials using Phaser were failed. The initial model was > obtained by ZN-SAD. Refinement was dome for space group P43212, with > cell parameters 31.96 31.96 95.07 90 90 90, with one duplex molecule > per AU. > > > Schreuder, Herman /DE wrote: > > > At this resolution, one sees many amino-acid side chains with > > alternative conformation, so it might be a good idea to test if > > this is also true for nucleotides. > > Dear Herman, > I'm working on some protein ultra-high resolution structures (around > 1.0 A or higher), and alternative conformations are nicely visible on > electron density maps. In this case, there is visible almost all > molecule, when you switch contouring to 2 sigma or lower on Fo-Fc > maps, so I think, in this case it's not the same situation. > > > Matthew Snee wrote: > > Maybe test the spacegroup with Zanuda, and reprocess with the most > > likely lower symmetry group. > > I guess the stats should improve if you identify a pseudo symmetry > > operator that is currently being treated as a true symmetry > > operator? > > Eleanor Dodson wrote: > > Sometimes ghost like this mean there is a spacegroup error - > > absences can be the result of the non-crystallographic translation > > and not be truly indicitive of the spacegroup. What is the possible > > spacegroup and what is the NC translation vector? > > Dear Matthew and Eleanor, > > I run Zanuda on my datasets, and the output (which is below) > suggested, that spacegroup is right chosen. > > Step 1. > R-factors for the starting model. > Transformation into a supergroup. > --------------------------------------------------------------------- > | Subgroup | Spacegroup | R.m.s.d. | Refinement in tested group > | | | | from the > |--------------------------------| | Ref | | starting > | Rigid | Restrained | | | | model, A > |----------|---------------------| | | | > | R | R | R-free | > |----------|------------|----------|----------|----------|----------| > | >> 10 | P 43 21 2 | 0.0002 | -- | 0.5107 | 0.4871 | > | 10 | P 43 21 2 | 0.0002 | -- | -- | -- | > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > Step 2. > Refinements in subgroups. > There are 8 subgroups to test. > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > | >> 10 | P 43 21 2 | 0.0002 | -- | 0.5107 | > 0.4871 | > --------------------------------------------------------------------- > | 1 | P 1 | 0.0883 | 0.5252 | 0.4985 | 0.4883 | > | 2 | C 1 2 1 | 0.0828 | 0.5447 | 0.5006 | 0.4877 | > | 3 | P 1 21 1 | 0.0824 | 0.5367 | 0.5018 | 0.4921 | > | 4 | P 1 21 1 | 0.0789 | 0.5292 | 0.4971 | 0.4846 | > | 6 | P 21 21 21 | 0.0956 | 0.5380 | 0.5064 | 0.4929 | > | 7 | P 43 | 0.0935 | 0.5183 | 0.4952 | 0.4835 | > | 9 | C 2 2 21 | 0.0908 | 0.5435 | 0.5042 | 0.4910 | > | 10 | P 43 21 2 | 0.0855 | 0.5427 | 0.5097 | 0.4913 | > --------------------------------------------------------------------- > | << 7 | P 43 | 0.0935 | 0.5183 | 0.4952 | 0.4835 | > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > Step 3. > Refinement of the best model. > Candidate symmetry elements are added one by one. > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > | >> 7 | P 43 | 0.0935 | 0.5183 | 0.4952 | > 0.4835 | > --------------------------------------------------------------------- > | 1 | P 1 | 0.0927 | 0.5293 | 0.4991 | 0.4950 | > | 8 | C 1 2 1 | 0.0848 | -- | 0.5017 | 0.4906 | > | 9 | C 2 2 21 | 0.0871 | -- | 0.5059 | 0.4928 | > | 10 | P 43 21 2 | 0.0919 | -- | 0.5180 | 0.5109 | > --------------------------------------------------------------------- > | << 10 | P 43 21 2 | 0.0919 | -- | 0.5180 | 0.5109 | > --------------------------------------------------------------------- > > R-factor in the original subgroup is (almost) the best. > The original spacegroup assignment seems to be correct. > > According the non-crystallography translation vector, there is an > output from xtriage: > > ----------------------------------------------------- > | XYZ | height | p-value(height) | > ----------------------------------------------------- > | 0.000, 0.000, 0.334 | 53.049 | 4.456e-05 | > | 0.000, 0.000, 0.167 | 28.966 | 1.681e-03 | > | 0.000, 0.000, 0.500 | 27.692 | 2.102e-03 | > ----------------------------------------------------- > > > Jon Cooper wrote: > > Hello, have you tried anisotropic B-factor refinement? It is > > usually very good at cleaning-up the difference map. At that sort > > of resolution, you may still have some way to go in the refinement > > since the R and R-free usually go to about half of what you have, > > at least with proteins. > > Dear Jon. Yes, I used anisotropic refinement as usually for this sort > of resolution (1.4 A or better). But it looks too high for this small > object and very high resolution, in my opinion. > > Best regards, > > Rafal > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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