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 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

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]