[ccp4bb] RES: [ccp4bb] Off-topic: hollow protein crystals
Thanks to all those who kindly answered my original message, both to the board and private. It seems that hollow crystals are rather common and as most people pointed out, may be due to fast growth. Indeed, ours grew overnight from a initial screening at room temperature and with very high protein concentration, so we are in the process of optimization at the moment. We also have tested the "drinking straws" in the picture in one of our beamlines and got diffraction to a fairly decent resolution and I am hopeful we will have the protein structure very soon. Kind regards, -Andre. De: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Em nome de Andre Ambrosio Enviada em: quarta-feira, 2 de junho de 2010 16:07 Para: CCP4BB@JISCMAIL.AC.UK Assunto: [ccp4bb] Off-topic: hollow protein crystals Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
Re: [ccp4bb] Off-topic: hollow protein crystals
Many times. Jan Dohnalek On Wed, Jun 2, 2010 at 9:07 PM, Andre Ambrosio wrote: > Dear all, > > > > We have recently obtained crystals from a small protein, and interestingly, > at least for me, they are hollow trigonal rods (please see pictures > attached). > > Just out of curiosity, has anybody ever seen such feature for protein > crystals before? > > > > Regards, > > -Andre. > > > > > > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Off-topic: hollow protein crystals
Dear Andre, Yes, hollow crystals are not very uncommon. We have recently also solved a structure at very high resolution using long hollow crystals. Initially the walls were very thin; we managed to make them thicker (and the hole correspondingly smaller) by standard fine-tuning of conditions. I didn't see any "special" effects arising from the hollowness. We just got higher resolution as we got more material to fill in some of the hole. Saridakis E; Giastas P; Efthymiou G; Thoma V; Moulis J-M; Kyritsis P; Mavridis I. M J Biol.Inorg. Chem. 2009;14(5):783-99. Best, Emmanuel - Original Message - From: Andre Ambrosio To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, June 02, 2010 10:07 PM Subject: [ccp4bb] Off-topic: hollow protein crystals Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
Re: [ccp4bb] Off-topic: hollow protein crystals
Hi Andre, We saw this type of crystals quite often during crystallization of our 300 kDa complex. To our experience these crystals diffract very poorly (~7-10 A) and anisotropically. They may have highly favorable crystal contacts in one direction than the other two directions and grow very fast in favorable direction. To our experience we could not improve the diffraction significantly for these crystals. However, it is possible that in case of small protein, the diffraction can be improved. Best luck, ravi Ravindra D. Makde present address: Scientific Officer E High Pressure & Synchrotron Radiation Physics Division Bhabha Atomic Research Centre, Trombay, Mumbai, India. Tel: +91-22-25506754 (Res.), "All that we are is the result of what we have thought. The mind is everything. What we think, we become" Buddha --- On Wed, 6/2/10, Andre Ambrosio wrote: From: Andre Ambrosio Subject: [ccp4bb] Off-topic: hollow protein crystals To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, June 2, 2010, 3:07 PM Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
Re: [ccp4bb] Off-topic: hollow protein crystals
On Wed, Jun 2, 2010 at 3:06 PM, Eric Larson wrote: > The authors need to take the initiative and let the PDB know when their > structures have been published. The correspondence from the PDB people when > they are curating the structure deposition says something along these lines: > Yes, and I've done this before - but apparently I forgot this time. *shrug* The only reason this surprises me is that the PDB is fairly aggressive about releasing entries after a year, whether or not they've been published. In the past they at least emailed me first; this time, they must have simply released the structure without notifying any of the authors. If they had actually bothered to contact me, I would have told them to update the citation. Next time I may just go with immediate release. -Nat
Re: [ccp4bb] Off-topic: hollow protein crystals
Andre I had same kind of crystal like in your picture. It diffracted around 2.7A. Even I had some crystals where one end was closed. Both hollow crystal or the closed end (part) crystal diffracted same. With regards Syed --- On Thu, 6/3/10, Andre Ambrosio wrote: From: Andre Ambrosio Subject: [ccp4bb] Off-topic: hollow protein crystals To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, June 3, 2010, 12:37 AM Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
Re: [ccp4bb] Off-topic: hollow protein crystals
(* which still shows "To be published", 3 years after we published it - does the PDB not figure this out automatically?) The authors need to take the initiative and let the PDB know when their structures have been published. The correspondence from the PDB people when they are curating the structure deposition says something along these lines: "When the primary citation associated with your entry is published, please notify us at depo...@deposit.rcsb.org and provide pubmed ID (if available), journal name, volume, page numbers, title and authors list." __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Wed, 2 Jun 2010, Nat Echols wrote: On Wed, Jun 2, 2010 at 12:07 PM, Andre Ambrosio wrote: We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Yes, I had very similar crystals once (PDB ID 2i6f*). They were in the I4 space group, and the lattice formed two solvent channels, one large, one small, which I assumed ran the entire length of the crystal. The chains adjacent to the large solvent channel were poorly ordered and nearly uninterpretable in some datasets, so my best guess is that the hollow crystals were the result of this disorder. Fortunately, it didn't appear to have any effect on the diffraction quality. -Nat (* which still shows "To be published", 3 years after we published it - does the PDB not figure this out automatically?)
Re: [ccp4bb] Off-topic: hollow protein crystals
On Wed, Jun 2, 2010 at 12:07 PM, Andre Ambrosio < andre.ambro...@cebime.org.br> wrote: > We have recently obtained crystals from a small protein, and > interestingly, at least for me, they are hollow trigonal rods (please see > pictures attached). > > Just out of curiosity, has anybody ever seen such feature for protein > crystals before? > Yes, I had very similar crystals once (PDB ID 2i6f*). They were in the I4 space group, and the lattice formed two solvent channels, one large, one small, which I assumed ran the entire length of the crystal. The chains adjacent to the large solvent channel were poorly ordered and nearly uninterpretable in some datasets, so my best guess is that the hollow crystals were the result of this disorder. Fortunately, it didn't appear to have any effect on the diffraction quality. -Nat (* which still shows "To be published", 3 years after we published it - does the PDB not figure this out automatically?)
Re: [ccp4bb] Off-topic: hollow protein crystals
Hollow crystals are common. They arise from fast growth and slow diffusion. The material adds to the end of the tube before it has a chance to enter the interior of the tube. Hollow crystals can cause a problem when freezing because the expansion of the solvent in the middle of the tube is usually different from the crystalline material. Hollow crystals are beautiful, but for best chances one should try to slow the crystal growth by using additives like glycerol. James On Jun 2, 2010, at 12:07 PM, Andre Ambrosio wrote: Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
[ccp4bb] Off-topic: hollow protein crystals
Kurt Krause's group solved a structure from hollow crystals: J. Mol. Biol. 2002 Apr 26;318(2):503-18. The crystal structure of Trichomonas vaginalis ferredoxin provides insight into metronidazole activation. Crossnoe CR, Germanas JP, LeMagueres P, Mustata G, Krause KL. From: Andre Ambrosio Reply-To: Andre Ambrosio Date: Wed, 2 Jun 2010 14:07:14 -0500 To: Conversation: [ccp4bb] Off-topic: hollow protein crystals Subject: [ccp4bb] Off-topic: hollow protein crystals Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
