Re: [ccp4bb] Plz suggest me

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 01 January 2008

Previous message:
Subject: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Mark A Saper saper {- at -} UMICH {- dot -} EDU
Date: 2008-01-01

Next message:
Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Mark A Saper saper {- at -} UMICH {- dot -} EDU
Date: 2008-01-01

Subject: Re: Plz suggest me
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-01-01

> We have crystallized a cyanobacterial phycoerythrin which having two (alpha
> subunit) in an assymetric unit and held together by only three hydrogen bonds.
> When we compare the A and B molecule the RMSD is 1.32. because they same
> sequences then how it is possible to that two molecules are deviated at such
> extent. now the question is are both the molecules are crystallographic dimer?
> are two molecules are structural subunit as alpha 1 and alpha2?
> Is there any problem in refinement ? The structure was refined at 2.6 A with
> R 0.23/0.28

it sounds as if you have refined the structure without restraining the NCS. at
2.6A you would have to justify that (typically by showing that you get a
considerably lower Rfree without restraints than you do with restraints).

see these papers from the last millennium:

- G J Kleywegt & T A Jones, "Where freedom is given, liberties are taken",
Structure, 3, 535-540 (1995).

- G J Kleywegt, "Use of non-crystallographic symmetry in protein structure
refinement", Acta Crystallographica, D52, 842-857 (1996).

- G J Kleywegt & A T Brunger, "Checking your imagination: applications of the
free R value", Structure, 4, 897-904 (1996).

- G J Kleywegt & T A Jones, "Model-building and refinement practice", Methods
in Enzymology, 277, 208-230 (1997).

- G J Kleywegt, "Experimental assessment of differences between related
protein crystal structures", Acta Crystallographica, D55, 1878-1884 (1999).

- G J Kleywegt, "Validation of protein crystal structures" (Topical review),
Acta Crystallographica, D56, 249-265 (2000).

reprints available from http://xray.bmc.uu.se/gerard/citation.html

--dvd

******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN

http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 01 January 2008

Previous message:
Subject: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Mark A Saper saper {- at -} UMICH {- dot -} EDU
Date: 2008-01-01

Next message:
Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Mark A Saper saper {- at -} UMICH {- dot -} EDU
Date: 2008-01-01