Dear Preeti,
Feel free to use PDB_REDO. You might even ask Robbie (the REDO man) for
some help. He normally is good at answering Email. But I suggest you
first use REDO yourself. Then there are several possibilities:
1) REDO fails too. in that case you must ask Robbie.
2) REDO solves the problem, and you understand what happened. Then
everybody is happy.
3) REDO solves the problem, but you don't understand why. Then you can
ask any seasoned crystallographer (can also be Robbie) to explain what
is going on.
Greetings
Gert
Ps, feel free too to use the WHAT IF structure validation server(s) at
swift.cmbi.ru.nl. Perhaps they discover something big that you have missed.
On 4-4-2016 12:49, Preeti Satya wrote:
> Hello,
>
> I am facing some problem when I am refining my structure. My data is of
> resolution 2.1. The R and Free R for the structure is 23 / 28 and the rms
> bond angle is 1.496 and rms bond length is 0.0103. During the initial
> phase of refinement, the R/ Free R decreased upto 23/ 28. But now as I am
> refining my structure, the R/ free R is geting
> increased instead of decrease along with increment in bond angle. What
> should I do to decrease the R / free R or can I deposit my data as it is.
> The native structure for the protein is well refined and already deposited.
> This structure is a complex structure of the same protein with some ligand.
>
> Regards,
> Preeti
>
> PI - Dr. S .Gourinath
> School Of life sciences
> JNU
> N.Delhi 110067
>
> http://www.jnu.ac.in/Faculty/gourinath/Lab_Members.htm
> ....
> knowledge is power. So go on achieving knowledge through out your life time.
>
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