I have rarely worked with such data, but when we did, we always kept to
the riding hydroge positions in for refinement. You can check the
important ones by calculating sfs without them and seeing how well they
fit the map. For important residues like ASPS in catalytic triads that
can be very revealing.
Eleanor
On 11/23/2010 02:12 PM, Mischa Machius wrote:
> We have a similar case. There is difference density, but only for some of the hydrogens (mostly methyl groups on Leu, Ile, Val, Ala). How does one decide which hydrogens to include in explicit refinement? The case in question has 0.99Å data (diffraction is significantly better, but data were collected to only 0.99Å).
> n model, but for the important ock whether the riding posnes, we would che
> Sorry, first time refining at that kind of resolution.
>
> Thanks! MM
>
>
> On Nov 23, 2010, at 3:03 AM, George M. Sheldrick wrote:
>
>> Even with SHELX, at 1.2A you should use a riding model for hydrogens and
>> not refine them freely. SHELX has a useful facility (OMIT $H or OMIT
>> followed by specific hydrogen atom names) to keep the hydrogen atoms in
>> the atom list but not include their contributions to the structure
>> factors. Then you can very easily see in a difference map (e.g. with
>> COOT) if there is density near their expected positions.
>>
>> George
>>
>> Prof. George M. Sheldrick FRS
>> Dept. Structural Chemistry,
>> University of Goettingen,
>> Tammannstr. 4,
>> D37077 Goettingen, Germany
>> Tel. +49-551-39-3021 or -3068
>> Fax. +49-551-39-22582
>>
>>
>> On Tue, 23 Nov 2010, Ed Pozharski wrote:
>>
>>> Not sure if all the sirs will concur (and it might be a good idea to ask
>>> madams also), but the answer is probably no. As far as protonation
>>> state goes (guess that is what you are after, not oxidation), a better
>>> strategy may be to look into the bond lengths between the appropriate
>>> heavy atoms that are affected by it. Make sure that you refine without
>>> restraints imposed on a particular bond and see if its length is closer
>>> to the one corresponding to protonated or deprotonated state.
>>>
>>> Cheers,
>>>
>>> Ed.
>>>
>>> On Mon, 2010-11-22 at 23:18 -0600, Kenneth Satyshur wrote:
>>>> Sirs:
>>>>
>>>> We are attempting to refine hydrogens on a ligand (which is 100 % occupied) and
>>>> has ~ 40 heavy atoms (CNO). The data is 1.2 A, 325 AA, 83335 data points in C2.
>>>> We have refined aniso and with H riding along (Rf= 17, R = 15) in CCP4. Can we individually
>>>> refine the protons on the ligand? Let them run free with the others along for the ride?
>>>> Or will they just run away at this
>>>> resolution? Can CCP4 even do this? Should we switch to Shelx or Phenix?
>>>> It is important to find out what the oxidation state is for the ligand at the pH
>>>> we crystallized the protein and complex.
>>>>
>>>> thanks
>>>>
>>>
>>>
>
> -----------------------------------------------------------------------
> Mischa Machius, PhD
> Director, Center for Structural Biology
> Assoc. Professor, Dept. of Pharmacology
> Member, Lineberger Comprehensive Cancer Center
> University of North Carolina
> 4079 Genetic Medicine
> CB#7365
> 120 Mason Farm Road
> Chapel Hill, NC 27599-7365, U.S.A.
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>
>
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