Re: [ccp4bb] Unidentified density in coot
Looks like you're on the twofold axis, which will make interpretation challenging. Anything you put in may end up being too close to itself in the neighboring AU. What happens if you put in a water and display the symmetry? On Mon, Jun 23, 2014 at 8:17 AM, Shanti Pal Gangwar gangwar...@gmail.com wrote: Dear All I have solved a structure of my protein at 3.0 A. The crystallization condition is consisting of PEG400, NaCl, MgCl2 and Sodium citrate. The protein was purified in HEPES buffer. I can see an unidentified electron density blob in coot and I am not able to figure out what it could be? I have attached the snapshot of that blob with this mail. I request everyone to please help me in identification of this blob. Thanking you in advance. Shanti Pal Best regards Shanti Pal Gangwar, Ph.D School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.com -- [This e-mail message may contain privileged, confidential and/or proprietary information of H3 Biomedicine. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.]
Re: [ccp4bb] Unidentified density in coot
Dear Shanti Looks like you’re looking down the symmetry axis - so this could simply be ‘noise’, or a superposition of two bound ligands on top of each other… what’s your cryo-protectant? With regards, Tony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ - - - - - - - - - - - - - - - - - - email: antony.oli...@sussex.ac.ukmailto:antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 http://www.sussex.ac.uk/lifesci/oliverlab http://tinyurl.com/aw-oliver - - - - - - - - - - - - - - - - - - On 23 Jun 2014, at 13:17, Shanti Pal Gangwar gangwar...@gmail.commailto:gangwar...@gmail.com wrote: Dear All I have solved a structure of my protein at 3.0 A. The crystallization condition is consisting of PEG400, NaCl, MgCl2 and Sodium citrate. The protein was purified in HEPES buffer. I can see an unidentified electron density blob in coot and I am not able to figure out what it could be? I have attached the snapshot of that blob with this mail. I request everyone to please help me in identification of this blob. Thanking you in advance. Shanti Pal Best regards Shanti Pal Gangwar, Ph.D School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.commailto:email%3agangwar...@gmail.com 2.png1.png
Re: [ccp4bb] Unidentified density in coot
Dear Shanti Pal, did you use ethylene glycol as cryoprotectant? It may even be there in small amounts in your PEG400 solution. As Nicholas and Tony have said, this could be noise (or could be distorted due to noise) as it's on a 2-fold axis. From those pictures, it looks to me like one molecule of ethylene glycol (Coot - Get Monomer - EDO). Don't forget to drop the occupancy to 0.5, though! Best Isaac On 23 June 2014 13:17, Shanti Pal Gangwar gangwar...@gmail.com wrote: Dear All I have solved a structure of my protein at 3.0 A. The crystallization condition is consisting of PEG400, NaCl, MgCl2 and Sodium citrate. The protein was purified in HEPES buffer. I can see an unidentified electron density blob in coot and I am not able to figure out what it could be? I have attached the snapshot of that blob with this mail. I request everyone to please help me in identification of this blob. Thanking you in advance. Shanti Pal Best regards Shanti Pal Gangwar, Ph.D School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.com
