You may also get some insights from TLS refinement. Regards Thierry
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett Sent: Monday, April 29, 2013 12:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit FYI, I do know of one example of a solved structure where some of the molecules in the ASU are poorly defined. In 1EKJ, 4 of the 8 molecules in the ASU have low B-factors (mid 30s) and 4 have high B-factors (50s-60s). In the unit cell these layers alternate. It is possible, if everything else has been excluded, that your crystal has a similar crystal-packing issue. Cheers, _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu<mailto:rrowl...@colgate.edu> On 4/29/2013 9:30 AM, sonali dhindwal wrote: Dear Eleanor, Thanks for the suggestion, I just checked on the Zanuda program, it is also giving P1 as the best possible spacegroup for the molecule. and by not refining well, I meant for the electron density which is broken at many places at main chain, and poor electron density for the side chains which are otherwise good in other chains. Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” ________________________________ From: Eleanor Dodson <eleanor.dod...@york.ac.uk><mailto:eleanor.dod...@york.ac.uk> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Sent: Monday, 29 April 2013 4:36 PM Subject: Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit There isnt much information here! Funny that 3 chains are poor - does that mean one and a half heterodimers? I presume you have checked spacegroup? Zanuda will test to see if any higher symmetry is present.. Eleanor On 29 April 2013 06:02, sonali dhindwal <sonali11dhind...@yahoo.co.in<mailto:sonali11dhind...@yahoo.co.in>> wrote: Dear All, We are working on a crystal structure with 12 molecules in an asymmetric unit. It is a heteromer and each chain is made up of two type of chains. Therefore there are 24 chains in an asymmetric unit. It is giving solution in P1. Rfactor and Rfree has reached 20.25 and 25.6 at a resolution of 1.8Angstrom All the chains are refining well and have good electron density except 3 chains which have very poor electron density in most of the region. Whereas, the crystal structure of variants of the same protein we have solved earlier refined well and has very good electron density in all the chains. What could be the possible reason for these three chains which are not refining properly. Any suggestions will be very useful. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
