Re: [ccp4bb] Structure help

- 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: Re: Structure help
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-08-15

Next message:
Subject: Re: "Dry" structures
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-16

Subject: Re: Structure help
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-08-16

Maybe it is really P43 but twinned, with probably only two molecules in
the asymmetric unit. You can easily check this by putting it into SHELXL
with the instructions TWIN 0 1 0 1 0 0 0 0 -1 and BASF 0.4, or with the
new phenix refine (still beta test I think). Or wait for the next REFMAC.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582

On Wed, 15 Aug 2007, Yanming Zhang wrote:

> Hi ,
> Please help me on this structure:
> Data 1.8A: cell 84.892 84.892 172.580 90 90 90 with tetrahedral index
> Space group: P43212 or P43, Final refinement Rfree indicates P43 is better so
> most likely P43(also the systematic absence indicate P43 is it)
> Matthew coeffient indicates: P43 3mol/a.u(2.58,52%) 2mol/a.u(3.87, 68%)
>
> MR: Both Molerep and Phaser find out 2mol/au initially. Refinement reaches
> Rfree 30% , R 27% finally. WE think, comparing with 1.8 resolution, The R and
> Rfree are too high. Also considering the 1.8A resolution, there should be 3
> molecules in total. So we engaged into the effort to find out the 3rd
> molecule.
>
> Phased MR by MOLREP did find out the 3rd, so did Phaser(fix two, find out the
> 3rd). Both solutions gave relatively poorer statistics but packing is perfect.
> The 3rd molecule, solved by phased MR of MOLREP and PHaser respectively, can
> not superpose showing slightly different orientations, but position is
> similar. Refinement indicates PHased MOLREP MR gives lower Rfree.
>
> Using totally 3 molecule, When I restrain or constrain NCS during
> refinement(used TLS),R free goes way up (R~30, Rfree > 36%). If I refine
> without NCS,R factors slip right away to 27/30 but this strange thing
> happens: two copies of the original solution refines very well - low B
> factors,very good looking map. The 3rd copy, however, B factors are high and
> the map is bad, no good density match with the model.And the 3rd molecule did
> no help to Rfree or R.
>
> Story ends with my questions:
> 1,It seems the 3rd copy non-exist or globally disordered, under this
> circumstance, can I say 'because of the 3rd molecule is globally disordered so
> Rfree and R stay high (2mol/a.u with Rfree 30% R 27%, 1.8A data)?
> 2,Anything I should worry about in the process finding out the 3rd?
> 3,Are there suggestions to further lower down Rfree (the reasonable Rfree
> should be around 22%)?
>
> THANKS
> Yanming
>

CCP4bb navigation

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

Previous message:
Subject: Re: Structure help
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-08-15

Next message:
Subject: Re: "Dry" structures
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-16