Re: [ccp4bb] good phasing, bad R-factors

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

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Subject: Re: Rotation angle and translation distance
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-04-14

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Subject: Re: good phasing, bad R-factors
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-04-14

Subject: Re: good phasing, bad R-factors
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2009-04-14

Vlad Smith schrieb:
> Hi all,
>
> I have run into an unusual problem and am looking for some help. I am
> working with a small protein that is 76 amino acids in length. I have
> collected anomalous data and have located the 4/5 selenomethionine sites

that's a lot

> using SHELX C/D and SHARP. The map that is produced from SHARP after dm is
> pretty nice. I can see secondary structure and side chains. I have

that's all very good

> submitted this map to PHENIX autobuild, and it was able to place about 85%
> of the model. I have extended the model to be 90% complete. Upon
> inspection of the model, the selenomethioine locations match both the
> sequence and the peaks in the anomalous difference fourier map. I was
> surprised to find that the model actually falls into 2 ASUs. When I start

there are often many different ways to delineate ASUs. As long as the
model does not clash with symmetry mates of itself, it should be ok.

> my refinement using phenix.refine and/or refmac, the R-factors start off in
> the mid .40s, but after a round of simulated annealing the R-free rises to

What is the quality of the data? (resolution, R-factors, I/sigma ) How
did you collect the data? (deltaphi, distance, detector, exposure,
detector, beamline) Are there signs of radiation damage?

> the mid .50s. I can go back and remove a section of the model, run a round
> of refinement, and have the density return for that section of the map,
> which I interpret as the phases being some what correct. Does anyone have
> any ideas on what would cause the R-free to be so high? Again, I emphasize

Hard to say. I would guess some kind of user error, like refining
against the wrong column of the mtz file, or some such. Or some problem
with the data that is masked by the very high level of anomalous signal.

> that the experimental map was of rather good quality.
>
> Thanks for your help,
> Vlad

--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, UniversitÃ¤t Konstanz, Box M647, D-78457 Konstanz

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CCP4bb navigation

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

Previous message:
Subject: Re: Rotation angle and translation distance
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-04-14

Next message:
Subject: Re: good phasing, bad R-factors
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-04-14