[ccp4bb] TLS Refinement on ~3 angstrom resolution structures

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Platform Manager at CIC-bioGUNE (Bilbao, Spain)
From: Aitor Hierro aitorhierro {- at -} GMAIL {- dot -} COM
Date: 2008-10-20

Next message:
Subject: terminal window
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2008-10-20

Subject: TLS Refinement on ~3 angstrom resolution structures
From: Jim Fairman fairman {- dot -} jim {- at -} GMAIL {- dot -} COM
Date: 2008-10-20

Hello everyone,

I have two structures of a protein bound to two different small molecules I
am trying to refine with REFMAC5 from CCP4 v6.0.0. One has a resolution of
3.2 and the other has a resolution of 2.9. If I use TLS refinement
parameters on these structures I can get the Rwork/Rfree down to 19.5/26.4
(3.2 angstrom) and 20.7/27.5 (2.9 angstrom). Without TLS refinement the
Rwork/Rfree are 21.2/29.1 (3.2 angstrom) 22.2/27.5 (2.9 angstrom). The
question I have is in regards to the Bfactors for these refinements. The
average Bfactors are approximately 100 for the 3.2 angstrom structure and 70
for the 2.9 angstrom structure (These are the residual Bfactors before using
TLSANL to calculate the full Bfactor with the addition of the TLS
contribution) according to Baverage from CCP4. These Bfactors seem very
high to me, are they acceptable for publication? Is TLS refinement
appropriate in my case with my resolution (I read a paper from Sandalova et
al. 2001 PNAS p 9533-8 where they performed TLS refinement at 3.0 angstrom
resolution)? Any suggestions are welcome!

Cheers, Jim

--
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfairman@utk.edu james.fairman@case.edu

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Platform Manager at CIC-bioGUNE (Bilbao, Spain)
From: Aitor Hierro aitorhierro {- at -} GMAIL {- dot -} COM
Date: 2008-10-20

Next message:
Subject: terminal window
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2008-10-20