[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
