[phenixbb] UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?

Zhou, Tongqing (NIH/VRC) [E] tzhou at mail.nih.gov
Tue May 8 10:49:09 PDT 2012

Hi Nat, Kelly, Kay and Jürgen,

I also prefer the I422 with 1 mol/ASU since all the analysis pointed to higher symmetry. I will refine with I422 and report back.


The xtriage log for I422 data says high combined Z-score:

  The quarter of Intensities *least* affected by the anisotropy correction show

    <I/sigI>                 :   3.45e+00

    Fraction of I/sigI > 3   :   4.09e-01     ( Z =     4.02 )

  The quarter of Intensities *most* affected by the anisotropy correction show

    <I/sigI>                 :   1.54e+00

    Fraction of I/sigI > 3   :   7.20e-02     ( Z =    12.06 )

The combined Z-score of    12.71 indicates that there probably is significant

systematic noise amplification that could possibly lead to artefacts in the

maps or difficulties in refinement




Tongqing Zhou, Ph.D.

Staff Scientist

Structural Biology Section

Vaccine Research Center, NIAID/NIH

Building 40, Room 4609B

40 Convent Drive, MSC3027

Bethesda, MD 20892

(301) 594-8710 (Tel)

(301) 793-0794 (Cell)

(301) 480-2658 (Fax)


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-----Original Message-----
From: Nathaniel Echols [mailto:nechols at lbl.gov]
Sent: Tuesday, May 08, 2012 1:25 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?

On Tue, May 8, 2012 at 10:08 AM, Kelly Daughtry <kddaught at bu.edu<mailto:kddaught at bu.edu>> wrote:

>> 1.    Is it really twinned since including twin-law in refinment gave

>> much better numbers?

>   I would say, it likely is twinned

Actually, Xtriage says not:

The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected.

The symmetry of the lattice and intensity however suggests that the input space group is too low. See the relevant sections of the log file for more details on your choice of space groups.

Twinned refinement can be deceptive because it often lowers the R-factors even if twinning isn't present - Garib Murshudov warns about this in his talks on the subject.



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