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Check solvent % - as suggested low solvent content means tight packing means poor signal.

Check matthews coefficient ? Do you expect several molecules?
As suggested - does the model form an oligamer? ( You need to be careful with these - sometimes you generate thm using both crystal and non-crystallographic symmetry..

Check possible alternate SGs.

Try pruning your model - look at it in CCP4MG and see if there are extruded loops..
And good luck!

Eleanor

PS - by the way - you are cutting your data very savagely..
CC1/2 > 0.5 acceptable.

On 9 February 2017 at 08:20, <[log in to unmask]> wrote:

Dear Madhurima,

 

Small protein structures can be very difficult to solve by MR due to an unfavorable ratio between inter- and intra-molecular vectors in the pattersons. I am currently also struggling with some data sets myself.

 

However, there are things you could (and should) try:

1)     If your search protein forms an oligomer, e.g. dimer, trimer etc., generate this oligomer and use this as a search model. Having a bigger search model will significantly increase your signal to noise ratio.

2)     Try as many different MR programs as you can lay your hand on. Sometimes one succeeds, where others fail. I would at least try phaser.

3)     Do not run the program(s) using the default parameters, but carefully read the manual and adjust the parameters based on the size and shape of your search protein. If your protein contains cysteines and/or methionines, you could look if there is any anomalous signal in your home source data. Getting higher resolution synchrotron data may not hurt as well.

 

Good luck!

Herman

 

 

Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Madhurima Roy
Gesendet: Donnerstag, 9. Februar 2017 05:18
An: [log in to unmask]
Betreff: [ccp4bb] Problem with MolRep

 

Hi all,

I have a small protein which is of 6 kDa including six histidine tag. The protein crystallized in the conditions given bellow :

a)  0.1M Sodium acetate trihydrate pH 4.6, 3M NaCl.

b)  0.1 M Bis-tris pH 5.5, 2M Ammonium sulphate.

The crystals are plate shaped in both conditions.We collected diffraction data at our home source using Rigaku RaxisIV and processed the data using XDS.


In spite of good homology, the protein structure cannot be solved by MolRep , the contrast is very low approx 1.65. The PDB Blast result is given below:


38.1(total score), 70%(query coverage) 1e-05 (E-value) and 50%(Identity) .

The screen shot of the statistics showing R factor and quality of fit in  CORRECT.LP file is enclosed below.

 

Kindly help.

Thanks in advance.

Madhurima