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Of course metal ions, So4 etc often lie on special positions - the insulin hexamer is generated around Zn atoms on the 3-fold axis. Eleanor On 12/09/2010 01:29 PM, Ian Tickle wrote: > Of course it's always possible for an asymmetric molecule (or part of > a molecule, such as a side-chain) to lie on or near a symmetry axis, > provided it's rotationally disordered with occupancy 0.5 (assuming a > 2-fold). In other words half the molecules are randomly distributed > over half of the asymmetric units in one orientation and the other > half are in the other a.u.s in the symmetry-related orientation, so > the copies never clash. The occupancy must be near 0.5 because if it > deviated much from that you would start to see breakdown of the > symmetry of the diffraction pattern (with higher Rmerge etc), and you > would likely conclude that the space group is actually a sub-group of > the original one without the symmetry axis. Obviously it will depend > on the quality of the data, the resolution and the scattering power of > the disorder part whether you are able in practice to detect such a > breakdown of symmetry. > > The question here though is whether an atom (say the CG of the ASP) of > the rotationally disordered molecule/part-molecule in such a situation > necessarily lies _on_ a special position. It would be pure > coincidence if it did, for the simple reason that there's absolutely > no reason why it should do so. In other words, because it has > occupancy 0.5 (obviously it must have the same occupancy as the atoms > that it's covalently bonded to, assuming there's no other disorder > present), it must be disordered and so doesn't have to obey the bulk > symmetry. In fact, it would be equally 'happy' slightly displaced > from the special position. There will be no significant minimum in > the internal energy of the system for a disordered atom on a special > position, because the reason it's disordered is that there are no > strong interactions with the surrounding atoms, which would favour one > possible orientation over the other. > > This is quite different from the original question posed by Gloria > where (I assume) we have a molecule on a special position where there > is no rotational disorder (it may still have occupancy disorder, i.e. > it may only be present in a fraction of the a.u.s). Here clearly the > occupancy may be> 0.5 for a 2-fold and so no clashes with the > symmetry mate(s) are permitted (assuming of course that the space > group is correct!). In this case the molecule itself must therefore > possess at least the symmetry of the special position, e.g. H2O or SO4 > for a 2-fold, as Ralf says. Being ordered (or at least not as > disordered) such a molecule must have strong interactions with its > neighbours, so any shift off the special position would likely result > in an increase in internal energy. > > Cheers > > -- Ian > > On Thu, Dec 9, 2010 at 11:26 AM,<[log in to unmask]> wrote: >> Hi Ralf& Gloria, >> >> It is of course all a matter of definition, but it happens now and again >> that an asymmetric ligand is lying on top of a twofold axis. This is >> usually modeled by fitting the ligand in two orientations at half >> occupancy. In one of the proteins I am working on there is the >> carboxylic acid group of an Asp sitting on a 2-fold axis. I have modeled >> the Asp with 2 alternative conformations: in conformation A, the Asp >> side chain would clash with itself over the 2-fold axis, thus if one >> protein molecule has the Asp in conformation A, the twofold related >> protein molecule must have the Asp in conformation B (or some other >> conformation). >> >> I do not know whether you would call this a Wyckoff position, but side >> chains of proteins do sit on top of crystallographic symmetry axes. >> >> Best, >> Herman >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of >> Ralf W. Grosse-Kunstleve >> Sent: Thursday, December 09, 2010 3:47 AM >> To: [log in to unmask] >> Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms >> >> Hi Gloria, >> >> My hobby is space group symmetry. >> My interest phenix development. >> >>> so I can't imagine a protein crystallographer would ever need to >>> apply the modulation function to a protein atom that happened to be >>> on one. >> >> That's true. Protein residues don't have internal symmetry, therefore >> they are not compatible with crystallographic special positions. >> (Wyckoff positions are enumerations of classes of special positions.) >> >> In the PDB molecules with internal symmetry are really rare, except for >> H2O and SO4. But these contribute so little to the total scattering that >> it isn't important to handle them in a special way. So Wyckoff positions >> remain foreign in the macromolecular context. >> >> Ralf >> >> >> >> >> ----- Original Message ---- >>> From: Gloria Borgstahl<[log in to unmask]> >>> To: [log in to unmask] >>> Sent: Wed, December 8, 2010 12:16:54 PM >>> Subject: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms >>> >>> I've gotten some interesting responses, that I will summarize for the >>> group later, but I thought I should clarify why I asked. >>> >>> I was worrying about this because I have been working out the steps >>> in how to determine the (3+1)D superspace group for a protein >> crystal. >>> The last step listed in IT vol C chapter 9.8, is to consider any >>> atoms that lie ON a Wyckoff position, and what restrictions this >>> would apply to the modulation function that is refined for each atom. >>> >>> My first reaction, was "Wyckoff positions?" I vaguely remember >>> those, my recollection from my experience was they were really cool, >>> but were usually in the solvent, so I can't imagine a protein >>> crystallographer would ever need to apply the modulation function to a >> >>> protein atom that happened to be on one. But to a crystallographer >>> working on a modulated mineral, it would happen all the time, I'll >> bet. >>> So maybe this was one more thing that just didn't really apply to >>> protein structures and lucky us we don't worry about this last step >>> (just as I never did model that solvent water that was on one, back >>> in the 90s). >>> >>> Then I thought, maybe I'm missing something, or there are special >>> cases out there (and so far I have heard of a disulfide bond on a >>> 2-fold connecting two homodimers). >>> >>> So I polled the collective knowledge of the great ccp4bb group. >>> >>> On Wed, Dec 8, 2010 at 10:57 AM, Gloria Borgstahl >>> <[log in to unmask]> >> wrote: >>>> My fellow crystallographers, >>>> I wanted to take a poll. >>>> >>>> How many of you have ever had a protein atom on a Wyckoff position >>>> (AKA a special position). >>>> What kind of molecules have you found at special positions (it >>>> would have to contain the symmetry of the special position, right?) >> >>>> I'm thinking it is impossible to have a protein atom at a special >>>> position or am I exposing my ignorance yet again... >>>> >>>> my experience is that only once I found an atom in a special >>>> position, it was a strange solvent molecule, that blew my mind for >>>> a while until I learned about special positions in crystallography. >>>> >>>> Looking forward to your responses, Gloria >>>> >>>> >>>> ******************************************************************** >>>> **** >>>> Gloria Borgstahl >>>> Eppley Institute for Cancer Research and Allied Diseases >>>> 987696 Nebraska Medical Center >>>> 10732A Lied Transplant Center >>>> Omaha, NE 68198-7696 >>>> >>>> http://sbl.unmc.edu >>>> Office (402) 559-8578 >>>> FAX (402) 559-3739 >>>> >>>> Professor >>>> Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA >>>> Metabolism, Modulated Crystals, Crystal Perfection >>>> Interests: Manga, Led Zepplin, Cold Play, piano, BRAN, RAGBRAI, >>>> golf and lately superspace groups >>>> >>>> ******************************************************************** >>>> **** >>>> >>> >>