Re: [ccp4bb] SOme wquestions about refining.......

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

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

Previous message:
Subject: Re: R32 data
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2008-10-02

Next message:
Subject: Re: resuspending precipitated protein
From: "Uitdehaag, J {- dot -} C {- dot -} M {- dot -} (Joost)" joost {- dot -} uitdehaag {- at -} SPCORP {- dot -} COM
Date: 2008-10-02

Subject: Re: SOme wquestions about refining.......
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-10-02

Fire up a recent version of coot and go through every step on the
validation menu - but most im protantly the Ramachandran plot, the
density fit analysis, unmodelled blobs, rotamer probabilities and
finally and most importantly difference maps peaks.

Then run molprobity (via the web site if you don't have it installed)
and read the things-to-do-list into coot.

Kevin

AA wrote:
> Hello everyone,
>
> Please forgive my ignorance about the field of crystallography. I have
> recently started to process the diffraction data of a protein with a ligand
> attached to it. we have the structure of this protein already known and also
> known with different ligands. the way I did it is as flllows:
>
> I process the images in mosflm and then integrate them using scala inccp4i.
> After that I do molecular replacement by phaser. and finally refine it using
> refmac. Am I doing it correctly?
>
> Now since I am completely new to all this, I have not much clue about the
> outputs I get and if they are correct or not. What are the key things you
> should be looking at in the log files generated by phaser and refmac? Till
> now I get overall R factor of 29.32 and Rfree of 34.94. Is this fine or can
> I improve it more? If yes then what do I do to further improve the
> statistics? What should be the RmsBond and Rms Angle values? Since the
> structure is already solved a number of times with different ligands, what
> final values should i aim for to get a decent density maps in which I can
> fit my ligand structure.
>
> Sorry for being so naive. Any sort of information or papers or links would
> be very helpful.
>
> Thanks a lot.
>
> AA
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: R32 data
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2008-10-02