Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units
You dont say whether the unit cells are the same? In cases like this I sbmit both sets of coordinates to PISA - to get the preferred biological unit and check whether each structure has similar contacts. PISA is distributed with CCP4 but the version at the EBI pdb gives prettier results! Eleanor On 23 January 2014 15:19, Yong Wang wang_yon...@lilly.com wrote: Gabriel, Could this be just different but equivalent way of defining the asu? Ignoring one of the two tetramers and just focusing on the one tetramer that looks different in your case, the following picture assumes objects ABCD form a tetramer and repeat themselves in P1. You can have one trimer (ABC) plus a D from a symmetry related object as enclosed in the blue box. Then the other equivalent assembly is two dimers (BD and AC) as enclosed in the red box. This assumes that the “void” you referred to actually contains electron density for one monomer, not real void as having empty density. The equivalent assembly of asu can happen to any crystal form but if you try to keep the equivalent molecules together, it may appear more easily in P1 due to the arbitrary origin shift in P1. Cheers, *Yong Wang, Ph.D. Research Advisor, Discovery Chemistry Research* Eli Lilly Company Phone: 317-655-9145 Lilly Corporate Center DC 0403 Fax: 317-651-6333 Indianapolis, IN 46285 wang_y...@lilly.com CONFIDENTIALITY NOTICE: This e-mail message from Eli Lilly and Company (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Gabriel Moreno *Sent:* Wednesday, January 22, 2014 3:50 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units Dear CCP4 Contributors, I have a bit of a mystery: Two co-crystals that I picked up from the same grid tray (the two conditions vary slightly in %PEG and [salt], both indexed as P1 (apo structure normally crystallizes in P3221). One dataset was indexed, integrated and scaled with HKL2000. The other was processed with MOSFILM (could not process in HKL2000). Downstream processing for both sets was done exactly the same in PHENIX. Though both asymmetric units contain two complete tetramers, the interesting thing is that the configuration of monomers is different between the solutions. One contains one complete tetramer, one trimer (with a void where the fourth monomer would be), and one monomer on off on its own. The asymmetric unit of the other dataset solution also contains a complete tetramer, but then has two dimers. Close analysis of contacts between symmetrically related molecules reveals that the crystal packing is exactly the same between the two solutions from the two datasets. Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other quality indices are also comparable between the two sets. Here's my question: Does this phenomenon reveal anything important, or is this type of thing just seen sometimes with P1 solutions from crystals of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel image001.png
Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units
Gabriel, Could this be just different but equivalent way of defining the asu? Ignoring one of the two tetramers and just focusing on the one tetramer that looks different in your case, the following picture assumes objects ABCD form a tetramer and repeat themselves in P1. You can have one trimer (ABC) plus a D from a symmetry related object as enclosed in the blue box. Then the other equivalent assembly is two dimers (BD and AC) as enclosed in the red box. This assumes that the void you referred to actually contains electron density for one monomer, not real void as having empty density. The equivalent assembly of asu can happen to any crystal form but if you try to keep the equivalent molecules together, it may appear more easily in P1 due to the arbitrary origin shift in P1. [cid:image001.png@01CF1824.9A115470] Cheers, Yong Wang, Ph.D. Research Advisor, Discovery Chemistry Research Eli Lilly Company Phone: 317-655-9145 Lilly Corporate Center DC 0403 Fax: 317-651-6333 Indianapolis, IN 46285 wang_y...@lilly.com CONFIDENTIALITY NOTICE: This e-mail message from Eli Lilly and Company (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gabriel Moreno Sent: Wednesday, January 22, 2014 3:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units Dear CCP4 Contributors, I have a bit of a mystery: Two co-crystals that I picked up from the same grid tray (the two conditions vary slightly in %PEG and [salt], both indexed as P1 (apo structure normally crystallizes in P3221). One dataset was indexed, integrated and scaled with HKL2000. The other was processed with MOSFILM (could not process in HKL2000). Downstream processing for both sets was done exactly the same in PHENIX. Though both asymmetric units contain two complete tetramers, the interesting thing is that the configuration of monomers is different between the solutions. One contains one complete tetramer, one trimer (with a void where the fourth monomer would be), and one monomer on off on its own. The asymmetric unit of the other dataset solution also contains a complete tetramer, but then has two dimers. Close analysis of contacts between symmetrically related molecules reveals that the crystal packing is exactly the same between the two solutions from the two datasets. Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other quality indices are also comparable between the two sets. Here's my question: Does this phenomenon reveal anything important, or is this type of thing just seen sometimes with P1 solutions from crystals of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel inline: image001.png
[ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units
Dear CCP4 Contributors, I have a bit of a mystery: Two co-crystals that I picked up from the same grid tray (the two conditions vary slightly in %PEG and [salt], both indexed as P1 (apo structure normally crystallizes in P3221). One dataset was indexed, integrated and scaled with HKL2000. The other was processed with MOSFILM (could not process in HKL2000). Downstream processing for both sets was done exactly the same in PHENIX. Though both asymmetric units contain two complete tetramers, the interesting thing is that the configuration of monomers is different between the solutions. One contains one complete tetramer, one trimer (with a void where the fourth monomer would be), and one monomer on off on its own. The asymmetric unit of the other dataset solution also contains a complete tetramer, but then has two dimers. Close analysis of contacts between symmetrically related molecules reveals that the crystal packing is exactly the same between the two solutions from the two datasets. Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other quality indices are also comparable between the two sets. Here's my question: Does this phenomenon reveal anything important, or is this type of thing just seen sometimes with P1 solutions from crystals of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel
Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units
Dear Gabriel - You don't say if the two crystals are essentially identical - do they have the same unit cell parameters? I would imagine so. The phenomenon you describe is very common with molecular replacement (is this how you solved it?) or with auto-tracing. Your two structures are, in fact, identical within the limits of error of the refinement - this is why they give the same R values. There is no crystallographic difference between monomer A and monomer A' which is related by a crystal symmetry transformation. Either one (but not both!) can be included in the asymmetric unit, but we generally pick a set of monomers that gives a compact, pleasing arrangement. I expect that both of your arrangements can be reorganized to give two complete tetramers, by taking the orphan monomers and applying crystal symmetry transformations (simple unit cell translations, for P1) to place them in the equivalent position that completes the desired tetramer. Coot (and most other graphics programs) will generate the symmetry-equivalent molecules for you and allow you to save them, then you can just extract chain A (for example) from one PDB file, and paste it into the other PDB file in place of the chain A that's already there. Feel free to contact me if that explanation wasn't clear. - Matt On 1/22/14 3:50 PM, Gabriel Moreno wrote: Dear CCP4 Contributors, I have a bit of a mystery: Two co-crystals that I picked up from the same grid tray (the two conditions vary slightly in %PEG and [salt], both indexed as P1 (apo structure normally crystallizes in P3221). One dataset was indexed, integrated and scaled with HKL2000. The other was processed with MOSFILM (could not process in HKL2000). Downstream processing for both sets was done exactly the same in PHENIX. Though both asymmetric units contain two complete tetramers, the interesting thing is that the configuration of monomers is different between the solutions. One contains one complete tetramer, one trimer (with a void where the fourth monomer would be), and one monomer on off on its own. The asymmetric unit of the other dataset solution also contains a complete tetramer, but then has two dimers. Close analysis of contacts between symmetrically related molecules reveals that the crystal packing is exactly the same between the two solutions from the two datasets. Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other quality indices are also comparable between the two sets. Here's my question: Does this phenomenon reveal anything important, or is this type of thing just seen sometimes with P1 solutions from crystals of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units
Dear Gabriel, Couldn't it simply be that your two crystals were indexed differently? If you could give their respective cell parameters, it will be possible to tell whether this is the case. With best wishes, Gerard. -- On Wed, Jan 22, 2014 at 12:50:03PM -0800, Gabriel Moreno wrote: Dear CCP4 Contributors, I have a bit of a mystery: Two co-crystals that I picked up from the same grid tray (the two conditions vary slightly in %PEG and [salt], both indexed as P1 (apo structure normally crystallizes in P3221). One dataset was indexed, integrated and scaled with HKL2000. The other was processed with MOSFILM (could not process in HKL2000). Downstream processing for both sets was done exactly the same in PHENIX. Though both asymmetric units contain two complete tetramers, the interesting thing is that the configuration of monomers is different between the solutions. One contains one complete tetramer, one trimer (with a void where the fourth monomer would be), and one monomer on off on its own. The asymmetric unit of the other dataset solution also contains a complete tetramer, but then has two dimers. Close analysis of contacts between symmetrically related molecules reveals that the crystal packing is exactly the same between the two solutions from the two datasets. Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other quality indices are also comparable between the two sets. Here's my question: Does this phenomenon reveal anything important, or is this type of thing just seen sometimes with P1 solutions from crystals of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units
Hi Gabriel - If the crystal contacts really are all the same, it sounds to me like your MR program may have just placed the monomers in different but equivalent symmetry-related positions between the two structures. Try moving the outlying monomers to the symmetrically related positions that would complete the tetramer. The PISA server may help with this. You could also do this from within COOT (Extensions PISA... PISA Assemblies...). Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jan 22, 2014, at 3:50 PM, Gabriel Moreno gabe.li...@gmail.com wrote: Dear CCP4 Contributors, I have a bit of a mystery: Two co-crystals that I picked up from the same grid tray (the two conditions vary slightly in %PEG and [salt], both indexed as P1 (apo structure normally crystallizes in P3221). One dataset was indexed, integrated and scaled with HKL2000. The other was processed with MOSFILM (could not process in HKL2000). Downstream processing for both sets was done exactly the same in PHENIX. Though both asymmetric units contain two complete tetramers, the interesting thing is that the configuration of monomers is different between the solutions. One contains one complete tetramer, one trimer (with a void where the fourth monomer would be), and one monomer on off on its own. The asymmetric unit of the other dataset solution also contains a complete tetramer, but then has two dimers. Close analysis of contacts between symmetrically related molecules reveals that the crystal packing is exactly the same between the two solutions from the two datasets. Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other quality indices are also comparable between the two sets. Here's my question: Does this phenomenon reveal anything important, or is this type of thing just seen sometimes with P1 solutions from crystals of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
