[ccp4bb] Very weird

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

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

Previous message:
Subject: Re: Cannot running NTA to purify the protein having His-tag?
From: joost {- dot -} uitdehaag {- at -} ORGANON {- dot -} COM
Date: 2007-03-01

Next message:
Subject: Re: process SeMet labelled data
From: molatwork {- at -} YAHOO {- dot -} ES
Date: 2007-03-01

Subject: Very weird
From: yzhang {- at -} MAILER {- dot -} SB {- dot -} FSU {- dot -} EDU
Date: 2007-03-01

Dear all,

I am sorry to trouble you again because I am facing a very weird
situation:

Three copies from Phaser are the right solutions based upon:
1, Rfree 42% R 39%
2, No packing clash
3, The packing within the 3 makes good sense
4, Density evenly distributed among the 3 copies even without NCS

Then fix these 3, asking Phaser to find one more (here I adopt the
strategy one copy at a time). Phaser did find one more, So now I have 4
copies in total.

Using the phase calculated from the previous 3 copies(because Rfree 42%),
the 4th copy can exactly match one junk of the density, even the side
chain matchs, demonstrating the 4th copy is correct.

Checking the crystallographic packing, The density which the 4th occupies,
is an extra density which did not account for by the previous 3 copies or
their symmetry mates.

No Clash exists

Then I use the 4 copies to do the refinement, forseeing that there will be
a huge Rfree drop from 42% because I account for the extra density using
the 4th copy. BUT TO MY SURPRISE, THE RFREE INCREASE TO 65%.

Can you teach me what is going wrong? Thank you
Yanming

CCP4bb navigation

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

Previous message:
Subject: Re: Cannot running NTA to purify the protein having His-tag?
From: joost {- dot -} uitdehaag {- at -} ORGANON {- dot -} COM
Date: 2007-03-01

Next message:
Subject: Re: process SeMet labelled data
From: molatwork {- at -} YAHOO {- dot -} ES
Date: 2007-03-01