[Xplor-nih] Ensemble calculation of denatured protein

[Marius Clore]

The attached file has everything you need to know.

The criteria you talk about were chosen based on common sense. They are not
hard and fast but good choices
Based on experimental error.

On 4/30/08 9:24 AM, "Jie-rong Huang" <jierongh at googlemail.com> wrote:

> Hi Charles, 
> 
> Some other questions :p
> Delta i (eq 14 in 2004 Iwahara JACS) was set to a minimum value of 1.0(/s) as
> mentioned in this paper.  However, the delta T2 I obtained is measured by
> conventional N-15 relaxation methods instead of yours (setGammaI was changed
> therein).  The delta T2 and error (from two repeated experiments fitting with
> several different relay times) are both smaller than 1H delta T2.  Any place I
> can change this setting?  Is that the reason I have some "VIOLATED" messages?
> For example, 
> #########
> --(selection 1)--
>          43  LEU   HN
> --(selection 2)--
>   ALT1   74 CYSP  OS1 , ALT2   74 CYSP  OS1 , ALT3   74 CYSP  OS1 , ALT4   74
> CYSP  OS1 , ALT5   74 CYSP  OS1 , ALT6   74 CYSP  OS1 , ALT7   74 CYSP  OS1 ,
> ALT8   74 CYSP  OS1 , ALT9   74 CYSP  OS1 , ALT0   74 CYSP  OS1
>  obs 0.9888 ( +/- 0.1651 )| calc 0.000172847 |  diff 0.988627
> VIOLATED
> weight factor : 11.2717
> reff : 47.7234
> S2angular: 0.985953
> S2radial:  0.939499
> S2:        0.926302
> #########
> 
> Besides, how was the criteria mentioned in 2004 Iwahara JACS (1H-Gamma2 >=
> 2delta for PREs with 1H-Gamma2 >=6; delta < 3.0 /s for PREs with 1H-Gamma2 < 6
> /s) chosen?  Thanks a lot!
> 
> Best wishes, 
> 
> Jie-rong
> 
> 


-- 
G. Marius Clore, MD, PhD
Chief, Protein NMR Section
Laboratory of Chemical Physics
Bldg 5/Rm B1-30I
NIDDK, National Institutes of Health
Bethesda, MD 20892-0520
Tel: (301) 496 0782
Fax: (301) 496 0825
E-mail: mariusc at intra.niddk.nih.gov
web: http://spin.niddk.nih.gov/clore

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