[ccp4bb] Phantom Crystals - a recap
Thanks to all who replied regarding experiences with phantom crystals (objects with crystal-like morphologies but NO diffraction). The answers were more fascinating than the original poorly worded inquiry deserved. Here is a recap. The observation of phantoms may be rare but not so rare: a number of people replied with first hand experience. Classes of compounds that may lead to these bad actors: membrane-associated proteins and RNAs. NO diffraction may be interpreted as no OBSERVABLE Bragg diffraction, but beware of behind-the-beamstop diffraction; i.e. a few Bragg peaks that are not typically observed unless care is taken to insure a small beamstop. I think of a mental image as follows. Say proteins are spherically shaped and present as cats' eyes marbles. You might be able to lay them down in a perfect HCP lattice but rotationally the eyes might point in all directions. The object at macroscopic dimensions would look like a crystal but at atomic dimensions there would be no buildup of scattering from cooperative effect of many atoms at the same lattice spacing. Thanks to all. George George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu
Re: [ccp4bb] Phantom Crystals - a recap
I would think that a perfect HCP lattice, no matter the disorder in the organization of the molecules, would lead to Bragg diffraction, albeit of low resolution. The ghost crystals probably consist of very imperfect lattice(s) which fluctuate in their dimensions and kind over space and time. Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: George DeTitta To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, June 23, 2009 12:37 PM Subject: [ccp4bb] Phantom Crystals - a recap Thanks to all who replied regarding experiences with phantom crystals (objects with crystal-like morphologies but NO diffraction). The answers were more fascinating than the original poorly worded inquiry deserved. Here is a recap. The observation of phantoms may be rare but not so rare: a number of people replied with first hand experience. Classes of compounds that may lead to these bad actors: membrane-associated proteins and RNAs. NO diffraction may be interpreted as no OBSERVABLE Bragg diffraction, but beware of behind-the-beamstop diffraction; i.e. a few Bragg peaks that are not typically observed unless care is taken to insure a small beamstop. I think of a mental image as follows. Say proteins are spherically shaped and present as cats' eyes marbles. You might be able to lay them down in a perfect HCP lattice but rotationally the eyes might point in all directions. The object at macroscopic dimensions would look like a crystal but at atomic dimensions there would be no buildup of scattering from cooperative effect of many atoms at the same lattice spacing. Thanks to all. George George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu
Re: [ccp4bb] Phantom Crystals - a recap
If I understand the idea correctly, I would still expect to see good Bragg spots, but the amplitudes would represent the rotationally averaged protein. This is like the hexagonal water lattice (Ih): there is disorder in how the water molecules are oriented at each lattice point (not really disorder, but more than one choice for orientation), but the structure is solvable and the resulting density is a spatial average where hydrogens appear to be nearly overlapping. I agree that the lattice itself has to be distorted or imperfect for the Bragg spots to go away. It would be interesting to see how much lattice distortion can occur before the spots are gone. Actually I'd like to be able to simulate stuff like this for several reasons. Not sure how to do it other than brute-force building a massive lattice of proteins and applying FFT directly. Maybe separate treatment of structure factor and form factor would be easier. Surely this has been done in the solid state/ small molecule/diffuse scattering literature ... Ideally a system where you can tweak a parameter to go from crystal lattice to solution scattering continuously. Richard I would think that a perfect HCP lattice, no matter the disorder in the organization of the molecules, would lead to Bragg diffraction, albeit of low resolution. The ghost crystals probably consist of very imperfect lattice(s) which fluctuate in their dimensions and kind over space and time. Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: George DeTitta To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, June 23, 2009 12:37 PM Subject: [ccp4bb] Phantom Crystals - a recap Thanks to all who replied regarding experiences with phantom crystals (objects with crystal-like morphologies but NO diffraction). The answers were more fascinating than the original poorly worded inquiry deserved. Here is a recap. The observation of phantoms may be rare but not so rare: a number of people replied with first hand experience. Classes of compounds that may lead to these bad actors: membrane-associated proteins and RNAs. NO diffraction may be interpreted as no OBSERVABLE Bragg diffraction, but beware of behind-the-beamstop diffraction; i.e. a few Bragg peaks that are not typically observed unless care is taken to insure a small beamstop. I think of a mental image as follows. Say proteins are spherically shaped and present as cats’ eyes marbles. You might be able to lay them down in a perfect HCP lattice but rotationally the eyes might point in all directions. The object at macroscopic dimensions would look like a crystal but at atomic dimensions there would be no buildup of scattering from cooperative effect of many atoms at the same lattice spacing. Thanks to all. George George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu
[ccp4bb] Fw: Re: [ccp4bb] Phantom Crystals
Note: Forwarded message attached -- Original Message -- From: Debajyoti Dutta debajyoti_dutt...@rediffmail.com To: deti...@hwi.buffalo.edu Subject: Re: [ccp4bb] Phantom Crystals---BeginMessage--- There may be a chance of getting crystal like formations. This I presume the ppt or transparent skin formation with some distinct shape. I had experienced with mounting some crystals (may be not) of particular shape which did bot yield a single Bragg spot. During my hanging drop experiment I discover that during crystallization process the crystal appears and the whole drop become covered by some transparent layer. It broke into several parts when I tried to mount the crystal. These broken shapes are so much like the crystal that I was confused about which one I desire. On Thu, 18 Jun 2009 03:40:46 +0530 wrote I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu ---End Message---
Re: [ccp4bb] Phantom Crystals
We do see these from time to time with users, but nobody pays attention to them. It once happened to us a number of years ago. They were perfectly good looking lysozyme crystals treated with heavy metal soak. They diffracted fine when fresh, but failed to diffract at all after a couple months of storage. I think Art Weaver studied these kinds of cases years ago using electron microscopy to see if there was any visible problem with the lattice. Check this out: A.J. Weaver, A.W. McDowall, D.B. Oliver, and J. Deisenhofer, J. Struct. Biol., 87 (1992). In Art's case, he was able to extract lattice and packing info from the FFT of the EM images (at 40 A). Perhaps if he had access to a SAXS line, he would have seen Bragg spots. Hard to know. It seems to me that there should always be some anisotropic scattering at very low angles no matter how badly the lattice is distorted. Richard Gillilan MacCHESS BTW, I've also seen and harvested ghost crystals that were bubbles. Folds of skin can look like crystal edges sometimes. Speaking of ghosts, I had a dried out drop that looked just like a statue of Buddha I thought. One of my students came upon one that looked just like a couple of monkeys kissing. The ACA should host a pareidolia contest someday. I’d appreciate it if people could tell me their experiences with what I would call “phantom crystals”, or “ghost crystals”. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don’t show a single Bragg spot.
Re: [ccp4bb] Phantom Crystals
MAD Scientist Thanks, V. Nagarajan JAN Scientific, Inc. http://janscientific.com -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: Thursday, June 18, 2009 11:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Phantom Crystals [deleted] Nevertheless, I think it is still up in the air how much diffraction tends to be degraded by crystal handling vs crystals just being born ugly, as the proper control (shooting crystals without handling them) has not been done on anything but a few test cases. In fact, I have heard enough stories about ugly crystals diffracting very well and beautiful crystals diffracting poorly to wonder if these two qualities really are anticorellated. That is, beauty really is just skin deep (and ugly goes to the core). I think it will be telling to see what sort of results we get from the now several available in-situ diffraction systems shameless plugone of which myself and others developed with Fluidigm, who are now selling them/shameless plug. -James Holton MAD Scientist
Re: [ccp4bb] Phantom Crystals
Zitat von George DeTitta deti...@hwi.buffalo.edu: I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) ... There is also a second type of ghost crystals, those which do not have edges at all, with a ball- or egg-like apearance and which diffract perfectly well! but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu
Re: [ccp4bb] Phantom Crystals
A few more examples of what Daniel refers to can be seen in Figure 11 - Nature Protocols 4:706-731, 2009. We encounter them from time to time using the in meso (lipidic cubic phase) method. With experience you get to recognize them for what they are. Martin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Daniel Picot Sent: 18 June 2009 08:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Phantom Crystals The object that approaches the most a ghost to my mind is a picture of a bubble trapped into a lipidic cubic phase of the detergent beta-octyl-glucoside, it can be found in the article from P. Sakya, J.M. Seddon R. Templer (1994) J.Phys II France 4:1311. I got also crystals of membrane protein (i.e. not bubble) in the same detergent that exhibited the same faceted cubic habits, they often disappeared quickly (a few days) and were to soft to be manipulated. Daniel George DeTitta a écrit : I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. **George T. DeTitta, Ph.D.** **Principal Research Scientist** **Hauptman-Woodward Institute** **Professor and Chairman** **Department of Structural Biology** **SUNY at Buffalo** **700 Ellicott Street Buffalo NY 14203-1102 USA** **(716) 898-8600 (voice)** **(716) 898-8660 (fax)** **www.hwi.buffalo.edu** http://www.hwi.buffalo.edu
Re: [ccp4bb] Phantom Crystals
Phantom Crystals can easily be achieved by failing to cryoprotect most any crystal, or by a few other common crystal handling methods, but I don't think this is what you were asking about. I do have users bring in what I call plastic crystals from time to time, but these crystals that don't diffract a single spot are relatively rare. Once every month or two I see a new one. (not counting repeat visits from users who are cursed with them) I always advise doing a 180-degree oscillation in such cases because sometimes it is a salt crystal that just happened to not have any reciprocal lattice points on the Ewald sphere. If this reveals a symmetrical pattern of a few very bright spots, then it can only mean a salt crystal. But, once in a while there really is no diffraction at all, and the user is left to ponder if it really was a very bad protein crystal or just a chunk of plastic that fell into their drop. Repeating the setup is the only way to really know. Also, I suspect that small beamstops reduce the number of samples that meet your criterion, as I have also seen plenty of crystals that don't diffract beyond 30 A, or even 50 A or 100 A, but still give off a few spots in a region that would be behind the beamstop on many diffractometers. Such samples are common enough that Ana Gonzalez has coined the term BBC (behind-beamstop crystallography) to refer to such experiments. Another way to make a phantom crystal is with radiation damage. If you blast any crystal long enough, all the spots will go away, leaving a SAXS pattern around the beamstop: http://bl831.als.lbl.gov/~jamesh/ribo_blast/diffraction.gif How useful this SAXS pattern is for deducing structural information remains to be seen, but since even naturally phantom crystals must still contain atoms, and atoms scatter x-rays, then SAXS signal from such objects could be useful. Nevertheless, I think it is still up in the air how much diffraction tends to be degraded by crystal handling vs crystals just being born ugly, as the proper control (shooting crystals without handling them) has not been done on anything but a few test cases. In fact, I have heard enough stories about ugly crystals diffracting very well and beautiful crystals diffracting poorly to wonder if these two qualities really are anticorellated. That is, beauty really is just skin deep (and ugly goes to the core). I think it will be telling to see what sort of results we get from the now several available in-situ diffraction systems shameless plugone of which myself and others developed with Fluidigm, who are now selling them/shameless plug. -James Holton MAD Scientist George DeTitta wrote: I’d appreciate it if people could tell me their experiences with what I would call “phantom crystals”, or “ghost crystals”. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don’t show a single Bragg spot. **George T. DeTitta, Ph.D.** **Principal Research Scientist** **Hauptman-Woodward Institute** **Professor and Chairman** **Department of Structural Biology** **SUNY at Buffalo** **700 Ellicott Street Buffalo NY 14203-1102 USA** **(716) 898-8600 (voice)** **(716) 898-8660 (fax)** **www.hwi.buffalo.edu** http://www.hwi.buffalo.edu
[ccp4bb] Phantom Crystals
I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu
Re: [ccp4bb] Phantom Crystals
Do you include detergent artifacts in your query (even those containing protein)? If so, you will be deluged... Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: George DeTitta To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, June 17, 2009 5:11 PM Subject: [ccp4bb] Phantom Crystals I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu
Re: [ccp4bb] Phantom Crystals
You want my whole life story? Briefly, RNA does this often, simply out of spite. William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott On Jun 17, 2009, at 3:11 PM, George DeTitta wrote: I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu
