[phenixbb] Weird large continuous positive density blob

Alex Lee alexlee198609 at gmail.com
Tue Apr 26 14:52:32 PDT 2016

Hi Pavel,

Thank you for your suggestions.

Yes, it's better to leave this density blob alone. I tried: 1. put buffer
molecule (Bis-Tris; P400); 2. put helix;  3. put a short peptides
corresponding a region of the C-terminal. Unfortunately, these tries did
not make the density disappear (sometimes the density partly disappear but
still significantly portion of it surround the model I put in), neither did
it improve R free.   So now I feel maybe it's safe just to leave it alone
and explain that even though I have 3 copies of molecule in A.S.U, two
copies has density for C terminal residue 72-89 but one copy does not have
the density for that part.

On Tue, Apr 26, 2016 at 12:56 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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.
> Pavel
> 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>
> 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>
> https://goo.gl/photos/R1SaHPKS6VLfcesb7
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