I agree that the difference density isn’t “noise". However, just because it’s not noise doesn’t mean that it is modellable (with an atomic model) — the crystallographic density is an average over billions of molecules, and if its not obvious at 1.6Å what is bound, then it’s probably a superposition of states (or a highly disordered molecule with large B-factors, which in this case amounts to pretty much the same thing). When it’s a superposition of states in solvent regions, there are too many free parameters to build a reliable model: you don’t know how many alternate conformations to model, or how many species of molecules there are. It could be 1 conformer of PEG with 1 superposed conformer of water or 2 of PEG + 1 of water or 1 of PEG + 1 of something else + 1 of water… or literally anything…

So unless you have some prior information as to what is bound, I would play it safe and model nothing — the conservative approach.

Thanks,
Nick

—————————————————

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri <[log in to unmask]> wrote:

Thanks Nick.

May be it is not that weak. The blue map contour level was set to 1.5. I have attached another image in which the blue map is contoured to 1.0. I feel the green density (contoured at 3.0) is not just some noise.

On 26 October 2017 at 20:38, Nick Pearce <[log in to unmask]> wrote:
Hi,

Given the weakness and shapelessness of the density I doubt it is "one conformation of one thing", but rather a superposition of "one or more conformations of one or more things”. If that is the case then there probably isn’t enough information in the electron density or enough prior information to restrain a modelling approach — i.e. you could build a model that fit the density, but you could never determine if it was “correct”. I would probably just leave that bit un-modelled.

Thanks,
Nick

—————————————————

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri <[log in to unmask]> wrote:

Dear Dr. Vaheh,

I tried fitting waters around Co but the positive density is still present even after refinement.

Thanks,
Vijaykumar

On 26 October 2017 at 20:19, Oganesyan, Vaheh <[log in to unmask]> wrote:

Water molecules completing Co coordination?

 

Regards,

 

Vaheh Oganesyan

www.medimmune.com

 

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Vijaykumar Pillalamarri
Sent: Thursday, October 26, 2017 10:24 AM
To: [log in to unmask]
Subject: [ccp4bb] Unknown electron density

 

Dear ccp4bb,

 

I am solving the structure of a 1.6 Angstrom data of a metallo protein. While everything else is straight forward, this density (see the picture) seems unfamiliar to me. I don't see any thing fits in the density. This density present just above Histidine-Cobalt. What ever I try to fit, the molecule clahes with histidine ( I mean the distance between His and molecule is <2 Angstrom). 

 

The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% glycerol.

 

Any suggestions?

 

Thanks,

Vijaykumar Pillalamarri

UGC-SRF

C/O: Dr. Anthony Addlagatta

Principal Scientist

CSIR-IICT, Tarnaka

Hyderabad, India-500007

Mobile: +918886922975

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--
Vijaykumar Pillalamarri
UGC-SRF
C/O: Dr. Anthony Addlagatta
Principal Scientist
CSIR-IICT, Tarnaka
Hyderabad, India-500007
Mobile: +918886922975




--
Vijaykumar Pillalamarri
UGC-SRF
C/O: Dr. Anthony Addlagatta
Principal Scientist
CSIR-IICT, Tarnaka
Hyderabad, India-500007
Mobile: +918886922975