Thanks Randy, The a cell edge is 56.118, so not exactly half of 30.86. I am currently refining using NCS cartesian restraints as Phil suggested. Then I will visually inspect the model as well as compare b-factors. Thanks for your suggestions, I will look into them.
-Yarrow > Hi, > > It's not uncommon for pseudosymmetry to be found together with twinning, > and the presence of pseudosymmetry perturbs the statistics used to test > for twinning. In that circumstance, as Phil suggests, a really good way > to see what is going on is to take the lower symmetry solution and see if > it really obeys higher symmetry, but you can do that either with > coordinates or calculated structure factors. > > Your NCS matrix specifies a 2-fold rotation around an axis that is about 1 > degree off the x axis. Whether that 1 degree matters or not depends on > how precisely the molecules are placed in the MR solution. If 30.8649 is > precisely half of the a-cell edge, then this corresponds to a 2(1) screw > axis, but whether or not that is crystallographic depends on whether the > origin of that axis is in the right place relative to the 2(1) you're > assuming is correct. Working all that out from coordinates can be a bit > of a challenge, which will really have you hitting the books! > > The other way we've approached this kind of problem is to take the Fcalcs > from an MR model (usually solved in P1 if possible to avoid making any > assumptions about which symmetry operators are correct) and then use > either pointless or xtriage to see if those Fcalcs obey higher symmetry. > Another good approach is to use the zanuda program in the CCP4 suite, > which is designed to answer questions about pseudosymmetry and other > related problems. > > Good luck! > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road > E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 15 Oct 2013, at 22:31, Yarrow Madrona <amadr...@uci.edu> wrote: > >> Thank you Dale, >> >> I will "hit-the-books" to better the rotation matrices. I am concluding >> from all of this that the space group is indeed P212121. So I still >> wonder >> why I have some outliers in the intensity stats for the two additional >> screw axis and why R and Rfree both drop by 5% when I apply a twin law >> to >> refinement in P21. >> >> Thanks for your help. >> >> -Yarrow >> >> >>> Since Phil is no doubt in bed, I'll answer the easier part. Your >>> second matrix is nearly the equivalent position (x,-y,-z). This >>> is a two-fold rotation about the x axis. You also have a translation >>> of about 31 A along x so if your A cell edge is about 62 A you have >>> a 2_1 screw. >>> >>> Dale Tronrud >>> >>> On 10/15/2013 12:29 PM, Yarrow Madrona wrote: >>>> Hi Phil, >>>> >>>> Thanks for your help. >>>> >>>> I ran a "Find-NCS" routine in the phenix package. It came up with what >>>> I >>>> pasted below: >>>> I am assuming the the first rotation matrix is just the identity. I >>>> need >>>> to read more to understand rotation matrices but I think the second >>>> one >>>> should have only a single -1 to account for a possible perfect 2(1) >>>> screw >>>> axis between the two subunits in the P21 asymetric unit. I am not sure >>>> why >>>> there are two -1 values. I may be way off in my interpretation in >>>> which >>>> case I will go read some more. I will also try what you suggested. >>>> Thanks. >>>> >>>> -Yarrow >>>> >>>> NCS operator using PDB >>>> >>>> #1 new_operator >>>> rota_matrix 1.0000 0.0000 0.0000 >>>> rota_matrix 0.0000 1.0000 0.0000 >>>> rota_matrix 0.0000 0.0000 1.0000 >>>> tran_orth 0.0000 0.0000 0.0000 >>>> >>>> center_orth 17.7201 1.4604 71.4860 >>>> RMSD = 0 >>>> (Is this the identity?) >>>> >>>> #2 new_operator >>>> >>>> rota_matrix 0.9994 -0.0259 0.0250 >>>> rota_matrix -0.0260 -0.9997 0.0018 >>>> rota_matrix 0.0249 -0.0025 -0.9997 >>>> tran_orth -30.8649 -11.9694 166.9271 >>>>> Hello Yarrow, >>>>> >>>>> Since you have a refined molecular replacement solution I recommend >>>>> using that rather than global intensity statistics. >>>>> >>>>> Obviously if you solve in P21 and it's really P212121 you should have >>>>> twice the number of molecules in the asymmetric unit and one half of >>>>> the >>>>> P21 asymmetric unit should be identical to the other half. >>>>> >>>>> Since you've got decent resolution I think you can determine the real >>>>> situation for yourself: one approach would be to test to see if you >>>>> can >>>>> symmetrize the P21 asymmetric unit so that the two halves are >>>>> identical. >>>>> You could do this via stiff NCS restraints (cartesian would be >>>>> better >>>>> than dihedral). After all the relative XYZs and even B-factors would >>>>> be >>>>> more or less identical if you've rescaled a P212121 crystal form in >>>>> P21. >>>>> If something violates the NCS than it can't really be P212121. >>>>> >>>>> Alternatively you can look for clear/obvious symmetry breaking >>>>> between >>>>> the two halves: different side-chain rotamers for surface side-chains >>>>> for example. If you've got an ordered, systematic, difference in >>>>> electron density between the two halves of the asymmetric unit in P21 >>>>> then that's a basis for describing it as P21 rather than P212121. >>>>> However if the two halves look nearly identical, down to equivalent >>>>> water molecule densities, then you've got no experimental evidence >>>>> that >>>>> P21 with 2x molecules generates a better model than P212121 than 1x >>>>> molecules. An averaging program would show very high correlation >>>>> between the two halves of the P21 asymmetric unit if it was really >>>>> P212121 and you could overlap the maps corresponding to the different >>>>> monomers using those programs. >>>>> >>>>> Phil Jeffrey >>>>> Princeton >>>>> >>>>> >>>> >>>> >>> >>> >> >> >> -- >> Yarrow Madrona >> >> Graduate Student >> Molecular Biology and Biochemistry Dept. >> University of California, Irvine >> Natural Sciences I, Rm 2403 >> Irvine, CA 92697 > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
