[phenixbb] Weird large continuous positive density blob

Pavel Afonine pafonine at lbl.gov
Tue Apr 26 12:56:31 PDT 2016

Hi Alex,

if packing/contacts make sense that may be something (even unexpected) 
from crystallization cocktail.

I guess Autobuild needs to know what to look for and build, otherwise 
given the resolution there may be impractically too many choices. And if 
you knew what it is then building it by hand in this case is easier.

If you have no idea what it is then perhaps it's better to leave this 
density blob alone rather than stick into it something that you are not 
confident about.


On 4/18/16 13:56, Alex Lee wrote:
> Dear Phenixbb members,
> I have a protein (90aa length) structure with 2.3A resolution and 
> space group P21 refined to Rfree/R to around 0.27 / 0.20. There are 3 
> protein dimers in one asym unit. For two dimers (chain A, B, C, D), I 
> can see clearly continuous electron density from residue 10 to residue 
> 89. However for the third dimer (chain E and F), I can only see 
> clearly continuous density between residue 10 to residue 72 and lost 
> tracing of the main chain.  I did see a large electron density blob 
> close to the third dimer. (https://goo.gl/photos/R1SaHPKS6VLfcesb7 ; 
> Green is positive density at 3 sigma and blue is FWT PHWT at 2sigma 
> and 1sigma ). I do not know how to explain this blob. It seems to me 
> that this blob is unlikely protein fragments (some parts of the blob 
> is so chunky). Even if it's true that it's certain protein fragment 
> between residue 73 to residue 89 of chain E or chain F, then the 
> position of this fragment is totally different from the position of 
> its fragment counterparts in chain A,B, C,D. I assume NCS copies (in 
> this case maybe 3 copies) should have the same morphology as to each 
> other.
> It also seems to me that this density is not from my crystal growth or 
> harvest conditions, which has: Bis-Tris; PEG3350; PEG400 and NaCl.
> I do not know if Phenix Autobuild could build this automatically for 
> me, but I'll try this later.
> Thanks in advance for any input on this.
> The density link is: https://goo.gl/photos/R1SaHPKS6VLfcesb7
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