[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:

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

Previous message:
Subject: Re: resuspending precipitated protein
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-10-01

Next message:
Subject: Re: Protein-DNA complex prepartion for crystallization
From: devendra srivastava dbcrystal {- at -} GMAIL {- dot -} COM
Date: 2008-10-01

Subject: SOme wquestions about refining.......
From: AA awaan686 {- at -} STUDENT {- dot -} OTAGO {- dot -} AC {- dot -} NZ
Date: 2008-10-01

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: resuspending precipitated protein
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-10-01

Next message:
Subject: Re: Protein-DNA complex prepartion for crystallization
From: devendra srivastava dbcrystal {- at -} GMAIL {- dot -} COM
Date: 2008-10-01