Re: [ccp4bb] The importance of USING our validation tools
In general, I think we should be careful about too strong statements, while in general structures with high solvent diffract to low-res, there are a few examples where they diffract to high res. Obviously, high solvent content means fewer crystal contacts, but if these few are very stable? Similarly, there are probably a few structures with a high percentage of Ramachandran outliers which are real and similarly for all other structural quality indicators. However, combinations of various of these probably do not exist and in any case, every unusual feature like this should be described and an attempt made to explain/analyse it, which in the case of the Nature paper that started this thread was apparently not done, apart from the rebuttal later (and perhaps in unpublished replies to the referees?). With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather than faith, I think the structure is held together by a real mechanism, which however I can't explain. Like in the structure Axel Brunger mentioned, there is appreciable diffuse scatter, which imo deserves to be analysed by someone expert in the matter (to whom, or anyone else, I would gladly supply the images which I should still have on a tape or CD in the cupboard...). For low-res version of one image see http://web.usc.es/~vanraaij/diff45kd.png and http://web.usc.es/~vanraaij/diff45kdzoom.png two possibilities I have been thinking about: 1. only a few of the tails are ordered, rather like a stack of identical tables in which four legs hold the table surfaces stably together, but the few ordered tails/legs do not contribute much to the diffraction. This raises the question why some tails should be stiff and others not; perhaps traces of a metal or other small molecule stabilise some tails (although crystal optimisation trials did not show up such a molecule)? 2. three-fold disorder, either individually or in microdomains too small to have been resolved by the beam used. For this I have been told to expect better density than observed, but maybe this is not true. we did try integrating in lower space groups P3, P2 instead of P321 with no improvement of the density, we tried a RT dataset to see if freezing caused the disorder and we tried improving the phases by MAD on the mercury derivative, but with no improvement in the density for the tail. Mark J. van Raaij Unidad de Bioquímica Estructural Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ On 24 Aug 2007, at 03:01, Petr Leiman wrote: - Original Message - From: Jenny Martin [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, August 23, 2007 5:46 PM Subject: Re: [ccp4bb] The importance of USING our validation tools My question is, how could crystals with 80% or more solvent diffract so well? The best of the three is 1.9A resolution with I/ sigI 48 (top shell 2.5). My experience is that such crystals diffract very weakly. You must be thinking about Mark van Raaij's T4 short tail fibre structures. Yes, the disorder in those crystals is extreme. There are ~100-150 A thick disordered layers between the ~200 A thick layers of ordered structure. The diffraction pattern does not show any anomalies (as far as I can remember from 6 years ago). The spots are round, there are virtually no spots not covered by predictions, and the crystals diffract to 1.5A resolution. The disordered layers are perpendicular to the threefold axis of the crystal. The molecule is a trimer and sits on the threefold axis. It appears that the ordered layers somehow know how to position themselves across the disordered layers. I agree here with Michael Rossmann that in these crystals the ordered layers are held together by faith. Mark integrated the dataset in lower space groups, but the disordered stuff was not visible anyway. He will probably add more to the discussion. Petr Any thoughts? Cheers, Jenny
[ccp4bb] alternating strong/weak intensities in reciprocal planes - P622
Dear all, Please, maybe you could give some suggestions to the problem below. 1) Images show smeared spots, but xds did a good job integrating them. The cell is 229, 229, 72, trigonal, and we see alternating strong and weak rows of spots in the images (spots near each other, but rows more separated, must be by c*). They were scaled with xscale, P622 (no systematic abscences), R_symm = 5.3 (15.1), I/sigI = 34 (14) and redundancy = 7.3 (6.8), resolution 2.8 A. Reciprocal space show strong spots at h, k, l=2n and weak spots at h, k, l=2n+1 (I mean, l=2n intensities are practically all higher than l=2n+1 intensities, as expected from visual inspection of the images). Within planes h, k, l=2n+1, the average intensity is clearly and much *higher at high resolution than at low resolution*. Also, within planes h, k, l=2n, a subjective observation is that average intensity apparently does not decay much from low to high resolution. The data were trucated with truncate, which calculated Wilson B factor to be 35 A**2. 2) Xtriage points a high (66 % of the origin) off-origin Patterson peak. Also, ML estimate of overall B value of F,SIGF = 25.26 A**2. 3) I suspect to have a 2-fold NCS parallel to a (or b), halfway the c parameter, which is almost crystallographic. 4) I submitted the data to the Balbes server which using pseudo-translational symmetry suggested some solutions, one with a good contrast to others, with a 222 tetramer, built from a structure with 40 % identity and 58% positives, of a well conserved fold. 5) I cannot refine below 49 % with either refmac5, phenix.refine or CNS. Maps are messy, except for rather few residues and short stretches near the active site, almost impossible for rebuilding from thereby. Strange, to me, is that all programs freeze all B-factors, taking them the program minimum (CNS lowers to almost its minimum). Might this be due to by what I observed in the reciprocal space as related in 1 ? If so, might my (intensity) scaling procedure have messed the intensities due to their intrinsic property to be stronger in alternating planes ? How to overcome this ? 6) I tried some different scaling strategies *in the refinement step*, no success at all. 7) A Patterson of the solution from Balbes also shows an off-origin Patteron at the same position of the native data, although a little lower. 8) Processed in P6, P312 and P321, all of course suggest twinning. I would thank suggestions, point to similar cases, etc... In fact, currently I wondered why refinement programs take B-factor to such low values Many thanks, Jorge
[ccp4bb] Strange diffraction images
What a beautiful and interesting diffraction pattern! To me, it seems that there is a blurred set of spots with different cell dimensions, although nearly the same, underlying the ordered diffraction pattern. A possible interpretation occurred to me, that the ordered part of the crystal is supported by a less-ordered lattice of slightly different dimensions, which, because the crystal is a like a layer-cake of 2-d crystals, need not be commensurable in the short range with the ordered lattice. The nicely-ordered cake part of the crystal you solved, but the frosting between is of a different, less ordered nature, giving rise to the diffuse pattern which has slightly different lattice spacing. I would have to see more images to know whether this apparent lattice-spacing phenomenon is consistent, but it at least seems that way to me from the images you put on the web. I would shudder to think of indexing it, however. All the best, Jacob Keller ps I wonder whether a crystal was ever solved which had two interpenetrating, non-commensurable lattices in it. That would be pretty fantastic. ==Original message text=== On Mon, 27 Aug 2007 5:57:45 am CDT Mark J. van Raaij wrote: In general, I think we should be careful about too strong statements, while in general structures with high solvent diffract to low-res, there are a few examples where they diffract to high res. Obviously, high solvent content means fewer crystal contacts, but if these few are very stable? Similarly, there are probably a few structures with a high percentage of Ramachandran outliers which are real and similarly for all other structural quality indicators. However, combinations of various of these probably do not exist and in any case, every unusual feature like this should be described and an attempt made to explain/analyse it, which in the case of the Nature paper that started this thread was apparently not done, apart from the rebuttal later (and perhaps in unpublished replies to the referees?). With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather than faith, I think the structure is held together by a real mechanism, which however I can't explain. Like in the structure Axel Brunger mentioned, there is appreciable diffuse scatter, which imo deserves to be analysed by someone expert in the matter (to whom, or anyone else, I would gladly supply the images which I should still have on a tape or CD in the cupboard...). For low-res version of one image see http://web.usc.es/~vanraaij/diff45kd.pngand http://web.usc.es/~vanraaij/diff45kdzoom.pngtwo possibilities I have been thinking about: 1. only a few of the tails are ordered, rather like a stack of identical tables in which four legs hold the table surfaces stably together, but the few ordered tails/legs do not contribute much to the diffraction. This raises the question why some tails should be stiff and others not; perhaps traces of a metal or other small molecule stabilise some tails (although crystal optimisation trials did not show up such a molecule)? 2. three-fold disorder, either individually or in microdomains too small to have been resolved by the beam used. For this I have been told to expect better density than observed, but maybe this is not true. we did try integrating in lower space groups P3, P2 instead of P321 with no improvement of the density, we tried a RT dataset to see if freezing caused the disorder and we tried improving the phases by MAD on the mercury derivative, but with no improvement in the density for the tail. Mark J. van Raaij Unidad de Bioquímica Estructural Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ On 24 Aug 2007, at 03:01, Petr Leiman wrote: - Original Message - From: Jenny Martin [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, August 23, 2007 5:46 PM Subject: Re: [ccp4bb] The importance of USING our validation tools My question is, how could crystals with 80% or more solvent diffract so well? The best of the three is 1.9A resolution with I/ sigI 48 (top shell 2.5). My experience is that such crystals diffract very weakly. You must be thinking about Mark van Raaij's T4 short tail fibre structures. Yes, the disorder in those crystals is extreme. There are ~100-150 A thick disordered layers between the ~200 A thick layers of ordered structure. The diffraction pattern does not show any anomalies (as far as I can remember from 6 years ago). The spots are round, there are virtually no spots not covered by predictions, and the crystals diffract to 1.5A resolution. The disordered layers are perpendicular to the threefold axis of the crystal. The molecule is a trimer and sits on the threefold axis. It appears that the ordered layers somehow know how to
Re: [ccp4bb] Strange diffraction images
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two interpenetrating,
non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
Re: [ccp4bb] Strange diffraction images
I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold
symmetric diffraction
pattern. It seems that this is entirely possible, if one gets roughly
Penrose-tile shaped oligomers
somehow. But wow, how would you solve that thing? I guess one would have to
modify software from
the small molecule or matsci folks.
Jacob
==Original message text===
On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote:
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two interpenetrating,
non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
===End of original message text===
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
Re: [ccp4bb] Strange diffraction images - PS
Apologies, part of my previous message was missing and part
appeared twice. Here is another try:
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
Re: [ccp4bb] Strange diffraction images
Very dumb question perhaps:
If there were two interpenetrating lattices of slightly different cell
dimensions, would we not
expect that the indexing program would leave out a lot of the spots as
unpredicted or uncovered?
Could someone clarify with respect to the diffraction pattern that has just
been posted (diff45..png)?
Raji
-Included Message--
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two
interpenetrating, non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
-End of Included Message--
Re: [ccp4bb] Strange diffraction images
The left-out spots would be the diffuse spots, which I assume were not
indexed/integrated. The
sharp spots were presumably used to solve the structure.
JPK
==Original message text===
On Mon, 27 Aug 2007 11:36:08 am CDT Raji Edayathumangalam wrote:
Very dumb question perhaps:
If there were two interpenetrating lattices of slightly different cell
dimensions, would we not
expect that the indexing program would leave out a lot of the spots as
unpredicted or uncovered?
Could someone clarify with respect to the diffraction pattern that has just
been posted (diff45..png)?
Raji
-Included Message--
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two
interpenetrating, non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
-End of Included Message--
===End of original message text===
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
[ccp4bb] Applying NCS Edits in Coot
Dear all, I am trying to use the NCS Edits in Coot to be able to move a range of residues from a molecule to the NCS related ones and the command (copy-residue-range-from-ncs-master-to others ) is not working. The fragment that I want to add to the NCS related molecules is at the N-terminus. When I type the order Coot says: ABORT: (unbound variable). Hope I have been clear enough! Thanks in advance, Maria
Re: [ccp4bb] Strange diffraction images
As a side note, Xtriage doesn't think things are twinned as was suggested for one some of the other diffraction patterns discussed earlier today. Hi Todd, Detection of twinning in the presence of pseudo translations / and or NCS parallel to the twin law is difficult and using model based techniques (RvsR statistic) could be usefull. Furthermore, I would like to point to Acta D 63, 926-930 with some pointers to literature regaring other 'weird' pathologies. HTH Peter
Re: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622
On possibility for #5, the B factors all dropping to the lower limit during refinement. If you are including all of your low resolution data (which you should) but have not used a model for the bulk solvent scattering of X-rays (which would be bad) then you will observe this result. The refinement program will attempt to overestimate the amplitudes of the high resolution Fc's to match the overestimated low resolution Fc's. Check you log files to ensure you bulk solvent correction is operating correctly. Dale Tronrud Jorge Iulek wrote: Dear all, Please, maybe you could give some suggestions to the problem below. 1) Images show smeared spots, but xds did a good job integrating them. The cell is 229, 229, 72, trigonal, and we see alternating strong and weak rows of spots in the images (spots near each other, but rows more separated, must be by c*). They were scaled with xscale, P622 (no systematic abscences), R_symm = 5.3 (15.1), I/sigI = 34 (14) and redundancy = 7.3 (6.8), resolution 2.8 A. Reciprocal space show strong spots at h, k, l=2n and weak spots at h, k, l=2n+1 (I mean, l=2n intensities are practically all higher than l=2n+1 intensities, as expected from visual inspection of the images). Within planes h, k, l=2n+1, the average intensity is clearly and much *higher at high resolution than at low resolution*. Also, within planes h, k, l=2n, a subjective observation is that average intensity apparently does not decay much from low to high resolution. The data were trucated with truncate, which calculated Wilson B factor to be 35 A**2. 2) Xtriage points a high (66 % of the origin) off-origin Patterson peak. Also, ML estimate of overall B value of F,SIGF = 25.26 A**2. 3) I suspect to have a 2-fold NCS parallel to a (or b), halfway the c parameter, which is almost crystallographic. 4) I submitted the data to the Balbes server which using pseudo-translational symmetry suggested some solutions, one with a good contrast to others, with a 222 tetramer, built from a structure with 40 % identity and 58% positives, of a well conserved fold. 5) I cannot refine below 49 % with either refmac5, phenix.refine or CNS. Maps are messy, except for rather few residues and short stretches near the active site, almost impossible for rebuilding from thereby. Strange, to me, is that all programs freeze all B-factors, taking them the program minimum (CNS lowers to almost its minimum). Might this be due to by what I observed in the reciprocal space as related in 1 ? If so, might my (intensity) scaling procedure have messed the intensities due to their intrinsic property to be stronger in alternating planes ? How to overcome this ? 6) I tried some different scaling strategies *in the refinement step*, no success at all. 7) A Patterson of the solution from Balbes also shows an off-origin Patteron at the same position of the native data, although a little lower. 8) Processed in P6, P312 and P321, all of course suggest twinning. I would thank suggestions, point to similar cases, etc... In fact, currently I wondered why refinement programs take B-factor to such low values Many thanks, Jorge
Re: [ccp4bb] Strange diffraction images
I believe Wayne Hendrickson's lab has had such a case with a 10-fold
symmetric mollusc hemocyanin crystal. This must have been in the early
90's and to my knowlwedge they were never able to solve the structure
even though it diffracted beyond 2 Anstrom.
I'm not sure if this work has been published but you can check the paper
describing a single domain of this protein complex or contact one of its
authors.
Bart
J Mol Biol. 1998 May 15;278(4):855-70.
Crystal structure of a functional unit from Octopus hemocyanin.
Cuff ME, Miller KI, van Holde KE, Hendrickson WA.
Jacob Keller wrote:
I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold symmetric diffraction
pattern. It seems that this is entirely possible, if one gets roughly Penrose-tile shaped oligomers
somehow. But wow, how would you solve that thing? I guess one would have to modify software from
the small molecule or matsci folks.
Jacob
==Original message text===
On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote:
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered lattice
of slightly
different dimensions, which, because the crystal is a like a layer-cake of 2-d
crystals, need not
be commensurable in the short range with the ordered lattice. The nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is consistent,
but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two interpenetrating,
non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
===End of original message text===
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
--
==
Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax:1-780-492-7521
==
Re: [ccp4bb] Strange diffraction images
I think if there had been a case of a protein quasicrystal, it would have made the cover of Nature Here are some papers about quasicrystals: 1: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14267-70. New perspectives on forbidden symmetries, quasicrystals, and Penrose tilings. Steinhardt PJ. Quasicrystals are solids with quasiperiodic atomic structures and symmetries forbidden to ordinary periodic crystals-e.g., 5-fold symmetry axes. A powerful model for understanding their structure and properties has been the two-dimensional Penrose tiling. Recently discovered properties of Penrose tilings suggest a simple picture of the structure of quasicrystals and shed new light on why they form. The results show that quasicrystals can be constructed from a single repeating cluster of atoms and that the rigid matching rules of Penrose tilings can be replaced by more physically plausible cluster energetics. The new concepts make the conditions for forming quasicrystals appear to be closely related to the conditions for forming periodic crystals. 2: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14271-8. Five-fold symmetry in crystalline quasicrystal lattices. Caspar DL, Fontano E. Institute of Molecular Biophysics, Florida State University, Tallahassee, 32306-3015, USA. [EMAIL PROTECTED] To demonstrate that crystallographic methods can be applied to index and interpret diffraction patterns from well-ordered quasicrystals that display non-crystallographic 5-fold symmetry, we have characterized the properties of a series of periodic two-dimensional lattices built from pentagons, called Fibonacci pentilings, which resemble aperiodic Penrose tilings. The computed diffraction patterns from periodic pentilings with moderate size unit cells show decagonal symmetry and are virtually indistinguishable from that of the infinite aperiodic pentiling. We identify the vertices and centers of the pentagons forming the pentiling with the positions of transition metal atoms projected on the plane perpendicular to the decagonal axis of quasicrystals whose structure is related to crystalline eta phase alloys. The characteristic length scale of the pentiling lattices, evident from the Patterson (autocorrelation) function, is approximately tau 2 times the pentagon edge length, where tau is the golden ratio. Within this distance there are a finite number of local atomic motifs whose structure can be crystallographically refined against the experimentally measured diffraction data. Jacob ==Original message text=== On Mon, 27 Aug 2007 2:02:36 pm CDT Bart Hazes wrote: I believe Wayne Hendrickson's lab has had such a case with a 10-fold symmetric mollusc hemocyanin crystal. This must have been in the early 90's and to my knowlwedge they were never able to solve the structure even though it diffracted beyond 2 Anstrom. I'm not sure if this work has been published but you can check the paper describing a single domain of this protein complex or contact one of its authors. Bart J Mol Biol. 1998 May 15;278(4):855-70. Crystal structure of a functional unit from Octopus hemocyanin. Cuff ME, Miller KI, van Holde KE, Hendrickson WA. Jacob Keller wrote: I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold symmetric diffraction pattern. It seems that this is entirely possible, if one gets roughly Penrose-tile shaped oligomers somehow. But wow, how would you solve that thing? I guess one would have to modify software from the small molecule or matsci folks. Jacob ==Original message text=== On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote: Some small molecule crystallographers have specialized in solving and refining structures that, exactly as you describe it, consist of two (or more) interpenetrating, non-commensurable lattices. The usual approach is to decribe the crystal in up to six dimensional space. The programs SAINT and EVALCCD are able to integrate such diffraction patterns and SADABS is able to scale them. However the case in point is probably commensurate. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 27 Aug 2007, Jacob Keller wrote: What a beautiful and interesting diffraction pattern! To me, it seems that there is a blurred set of spots with different cell dimensions, although nearly the same, underlying the ordered diffraction pattern. A possible interpretation occurred to me, that the ordered part of the crystal is supported by a less-ordered lattice of slightly different dimensions, which, because the crystal is a like a layer-cake of 2-d crystals, need not be commensurable in the short range with the ordered lattice. The nicely-ordered cake part of the crystal you
Re: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622
Hi Jorge, The strong h, k, l=2n and weak h, k, l=2n+1 pattern suggest pseudo body centering. Does the off-origin Patterson peak lie at/near 0.5 0.5 0.5? You could get pseudo body centering if an NCS 2-fold lies parallel to a crystallographic 2(1) or 6(3) screw axis, with the NCS 2-fold a quarter (not half) of a unit cell distant from the crystallographic axis. The fact that you get good merging statistics in P622 even at the high resolution limit suggests to me that you either have that space group or a lower symmetry subgroup with a nearly 0.5 twin fraction. Even if you figure out completely what your pathological crystal conditions are it may be hard to refine the structure properly. In some cases crystals can snap from a pseudo- to a proper crystal by adding the right additive. This may be worth trying while you break your head on this case. One problem is that whenever you make a model that obeys the pseudo body centering you are going to get a significant R-factor and correlation coefficient, even if the actual model is wrong. If you get a clear rotation function solution, which is not affected by the pseudo translation, it may still work but otherwise it could be hard to know if you got the right solution or not. Trying a whole bunch of rotation function solutions and see which one will refine to a significantly lower R-free is one thing to try. Bart Jorge Iulek wrote: Dear all, Please, maybe you could give some suggestions to the problem below. 1) Images show smeared spots, but xds did a good job integrating them. The cell is 229, 229, 72, trigonal, and we see alternating strong and weak rows of spots in the images (spots near each other, but rows more separated, must be by c*). They were scaled with xscale, P622 (no systematic abscences), R_symm = 5.3 (15.1), I/sigI = 34 (14) and redundancy = 7.3 (6.8), resolution 2.8 A. Reciprocal space show strong spots at h, k, l=2n and weak spots at h, k, l=2n+1 (I mean, l=2n intensities are practically all higher than l=2n+1 intensities, as expected from visual inspection of the images). Within planes h, k, l=2n+1, the average intensity is clearly and much *higher at high resolution than at low resolution*. Also, within planes h, k, l=2n, a subjective observation is that average intensity apparently does not decay much from low to high resolution. The data were trucated with truncate, which calculated Wilson B factor to be 35 A**2. 2) Xtriage points a high (66 % of the origin) off-origin Patterson peak. Also, ML estimate of overall B value of F,SIGF = 25.26 A**2. 3) I suspect to have a 2-fold NCS parallel to a (or b), halfway the c parameter, which is almost crystallographic. 4) I submitted the data to the Balbes server which using pseudo-translational symmetry suggested some solutions, one with a good contrast to others, with a 222 tetramer, built from a structure with 40 % identity and 58% positives, of a well conserved fold. 5) I cannot refine below 49 % with either refmac5, phenix.refine or CNS. Maps are messy, except for rather few residues and short stretches near the active site, almost impossible for rebuilding from thereby. Strange, to me, is that all programs freeze all B-factors, taking them the program minimum (CNS lowers to almost its minimum). Might this be due to by what I observed in the reciprocal space as related in 1 ? If so, might my (intensity) scaling procedure have messed the intensities due to their intrinsic property to be stronger in alternating planes ? How to overcome this ? 6) I tried some different scaling strategies *in the refinement step*, no success at all. 7) A Patterson of the solution from Balbes also shows an off-origin Patteron at the same position of the native data, although a little lower. 8) Processed in P6, P312 and P321, all of course suggest twinning. I would thank suggestions, point to similar cases, etc... In fact, currently I wondered why refinement programs take B-factor to such low values Many thanks, Jorge -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==
Re: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622
Hi Jorge, I imagine your 222 tetramer makes a sort of 'pancake' which fits into a cell of 229x229x36 when you apply the 6-fold symmetry. If that was the case in the crystal, then these would be the cell dimensions that you would get. But I suspect you have a situation where the cell repeat has a pancake that is either slightly shifted in the plane normal to the 6-fold, or rotated out of that plane by a small number of degrees. So the crystal would have a doubled unit-cell, with the weak inter-layers. If the two pancakes had been exactly parallel, and exactly 36A apart, the weak layers would have disappeared completely, and the situation would reduce to the smaller cell. Because of the slight translation/rotation between two adjacent smaller cells, you get the weaker layers. The perturbation must be really small that it is much less noticeable at low res, which is where you see the weak reflections in the l=2n+1 layers. As the res goes up, the ability to discern the differences goes up, giving the more intense spots in the outer part of the diffraction pattern. This situation would still occur in the presence of systematic absences due to an unidentified screw axis, as suggested by another contributor. You can try for better ordered crystals, as suggested by someone else. But to rescue this data set, I would look for one good MR solution, then use it as a fixed solution and use the same rotation solution (or one very close to it) to find a second translation solution. This should be within a small fraction of 0,0,0.5. After rigid body refinement, you might see the rotation of the 'pancake' clearly. But to get acceptable R-factors, you must try all the screw axis combinations, 6, 6(1), 6(2), 6(3), 6(4) and 6(5). With a bit of luck, one of these will be much better than the others. One final remark: You seem to have cut off the res at 2.8A despite the significant I/sig(I) statistic in the outer shell, combined with a benign R-merge. This is understandable if it is due to geometry, but really, you must go for higher res, and maybe you will get an even clearer answer. If your data collection system is limiting for the above cell dimension and res combination, you should try a different facility, with a larger detector or shorter wavelength, or both. Synchrotrons are usually good for this sort of thing (of course I am advertising!). Good Luck. Pierre *** Pierre Rizkallah, Daresbury Laboratory, Warrington, Cheshire WA4 4AD, U.K. Phone: (+)44 1925 603808 Fax: (+)44 1925 603124 e-mail: [EMAIL PROTECTED] html: http://www.srs.ac.uk/px/pjr/ -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jorge Iulek Sent: 27 August 2007 12:48 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622 Dear all, Please, maybe you could give some suggestions to the problem below. 1) Images show smeared spots, but xds did a good job integrating them. The cell is 229, 229, 72, trigonal, and we see alternating strong and weak rows of spots in the images (spots near each other, but rows more separated, must be by c*). They were scaled with xscale, P622 (no systematic abscences), R_symm = 5.3 (15.1), I/sigI = 34 (14) and redundancy = 7.3 (6.8), resolution 2.8 A. Reciprocal space show strong spots at h, k, l=2n and weak spots at h, k, l=2n+1 (I mean, l=2n intensities are practically all higher than l=2n+1 intensities, as expected from visual inspection of the images). Within planes h, k, l=2n+1, the average intensity is clearly and much *higher at high resolution than at low resolution*. Also, within planes h, k, l=2n, a subjective observation is that average intensity apparently does not decay much from low to high resolution. The data were trucated with truncate, which calculated Wilson B factor to be 35 A**2. 2) Xtriage points a high (66 % of the origin) off-origin Patterson peak. Also, ML estimate of overall B value of F,SIGF = 25.26 A**2. 3) I suspect to have a 2-fold NCS parallel to a (or b), halfway the c parameter, which is almost crystallographic. 4) I submitted the data to the Balbes server which using pseudo-translational symmetry suggested some solutions, one with a good contrast to others, with a 222 tetramer, built from a structure with 40 % identity and 58% positives, of a well conserved fold. 5) I cannot refine below 49 % with either refmac5, phenix.refine or CNS. Maps are messy, except for rather few residues and short stretches near the active site, almost impossible for rebuilding from thereby. Strange, to me, is that all programs freeze all B-factors, taking them the program minimum (CNS lowers to almost its minimum). Might this be due to by what I observed in the reciprocal space as related in 1 ? If so, might my (intensity) scaling procedure have messed the intensities due to their intrinsic property to be
