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 >
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