Re: [ccp4bb] high TFZ score but 50% of Rfree

[Diana Tomchick]

Do the following.

1) Perform density modification (NCS averaging and solvent flattening)
2) Run the new phases through a model building program (Buccaneer works for all 
resolutions, Arp/wArp works well for better than ~2.7 Å or better resolution)

If this doesn’t give you a better quality model (meaning one that has 
identifiable secondary structure and an R-free below about 45%), then you need 
to go back to square one and examine your assumptions regarding data quality, 
Laue symmetry and space group, MR solution, etc.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Nov 17, 2017, at 2:23 PM, Yue Li 
<17ef008f608c-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Dear all,

I have several datasets (one best resolution reaching 2.2A), giving C2 space 
group, two molecules in an asymmetry unit (65.1% of solvent content).  When 
running MR using a template (<20% sequence identify to the target molecule), I 
got a solution with high TFZ (23.7) and LLG (842). However, the Rfree sticks to 
50% in the structural refinement using phenix. There is no complain in Xtriage 
- no twin, no translational NCS.  I think that the structure solution looks 
reasonable, which can explain the three disulfide bond formations through the 
sequence threading.  I tried to search three molecules in the asymmetry unit, 
but the final solution gives me two molecules.

Do you have any suggestion for this high Rfree problem?

Thank you very much for your help.

All the very best,

Simon




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] high TFZ score but 50% of Rfree

[Phil Jeffrey]

R=50% at a resolution of 2.2 Å is a lot different to 50% at, say, 3.5 Å 
resolution.  What happens if you refine it at 3.0 or 3.5 Å ?


What's the model vs sequence % identity ?

Phil Jeffrey
Princeton


On 11/17/17 3:23 PM, Yue Li wrote:

Dear all,

I have several datasets (one best resolution reaching 2.2A), giving C2 
space group, two molecules in an asymmetry unit (65.1% of solvent 
content).  When running MR using a template (<20% sequence identify to 
the target molecule), I got a solution with high TFZ (23.7) and LLG 
(842). However, the Rfree sticks to 50% in the structural refinement 
using phenix. There is no complain in Xtriage - no twin, no 
translational NCS.  I think that the structure solution looks 
reasonable, which can explain the three disulfide bond formations 
through the sequence threading.  I tried to search three molecules in 
the asymmetry unit, but the final solution gives me two molecules.


Do you have any suggestion for this high Rfree problem?

Thank you very much for your help.

All the very best,

Simon

[ccp4bb] high TFZ score but 50% of Rfree

[Yue Li]

Dear all,
I have several datasets (one best resolution reaching 2.2A), giving C2 space 
group, two molecules in an asymmetry unit (65.1% of solvent content).  When 
running MR using a template (<20% sequence identify to the target molecule), I 
got a solution with high TFZ (23.7) and LLG (842). However, the Rfree sticks to 
50% in the structural refinement using phenix. There is no complain in Xtriage 
- no twin, no translational NCS.  I think that the structure solution looks 
reasonable, which can explain the three disulfide bond formations through the 
sequence threading.  I tried to search three molecules in the asymmetry unit, 
but the final solution gives me two molecules.
Do you have any suggestion for this high Rfree problem?
Thank you very much for your help.
All the very best,
Simon