From: Jrh
Date: 16 December 2011 17:37
Jrh correction:- in the last sentence the final statistical test must involve the comparison of each of the two different dictionary distance values in turn (essentially assumed to be exactly known for simplicity) versus the experimentally derived distance and its DPI derived sigma (L).
Greetings,
John
Prof John R Helliwell DSc
On 16 Dec 2011, at 16:07, John R Helliwell wrote:
> Dear Bie Gao,
> You can obtain an estimate of the standard deviation on your putative
> Mg to ligand distance using the diffraction precision index (DPI)
> approach of Cruickshank and Blow (1999 and 2002 Acta Cryst D). ie:-
> D M Blow Acta Cryst. (2002). D58, 792-797
> Synopsis: The formulae for the diffraction-component precision index
> introduced by Cruickshank [(1999), Acta Cryst. D55, 583-601] are
> simplifed using two approximations. A rearranged formula for the
> precision index is presented which can readily be calculated from
> experimental data.
>
>
> Using this you can add a quantitative test of statistical significance
> to the, of course, very senible earlier inputs to your questions. Do
> note though that the DPI is calculated as a number for the position
> error, sigma (x), on an atom with an average B factor. You have to
> adjust your DPI value for the atoms in question via the square root of
> their B value ratioed to the average B. For example a lower than
> average B gives a more precise sigma (x) than the average. Finally the
> sigma on the bond distance itself is calculated from the sigma (x)
> pair of values for each atom via the quadrature formula. The usual
> statistical test of significance is if the ligand distance (L) is then
>> 3sigma (L).
>
> Best wishes,
> Prof John R Helliwell DSc.
>
> On Thu, Dec 15, 2011 at 9:29 PM, bie gao wrote:
>> Thank you all for the help. These are the key factors I collected so far:
>> 1. Distance, Mg--O is shorter (2.0 -- 2.4A)
>> 2. Coordination, Mg is octahedrally coordinated.
>> 3. B factors, local B factors (i.e. the residues that coordinate with the
>> ion) should be similar.
>> 4. Use Mn++ to replace Mg.
>> I will look into these more.
>>
>> Best,
>> Gao
>>
>>
>> On Wed, Dec 14, 2011 at 5:45 PM, bie gao wrote:
>>>
>>> Hi every,
>>>
>>> I'm working with 2 crystal forms of a protein from 2 different
>>> crystallization conditions. Condition 1 has 100mM MgCl2. Condition 2
>>> doesn't. Both are ~2.9 angstrom. The 2 structures are virtually identical
>>> except in condition1, there is a clear positive density surrounded by a Glu
>>> side chain carboxyl and a couple of main carboxyl groups. (Again, condition
>>> 2 doesn't have this density).
>>>
>>> My initial thought is that a Mg atom is incorporated and it fits well. But
>>> the problem is we can not role out the possibility of a water molecule.
>>> Refining with Mg gives a b-factor of 42 (about average for the whole
>>> protein). The b-factor is 21 when refining with a water. Both cases there is
>>> no positive/negative density at contour=2.0.
>>>
>>> Based on the current data, is there any other role we can apply to see how
>>> likely it is a Mg or water. Or anomalous scattering is the only way? Thanks
>>> for your suggestions.
>>>
>>> Best,
>>> Gao
>>
>>
>
>
>
> --
> Professor John R Helliwell DSc
----------
From: Yuri Pompeu
In my personal opinion, whatever that is worth, I would question why you are modelling a Mg2+ ion if you are having to go through some trouble to prove it is there. If you dont see octahedral coordination to waters and or Asp/Glu it probably is not a Mg.
HTH
Date: 16 December 2011 17:37
Jrh correction:- in the last sentence the final statistical test must involve the comparison of each of the two different dictionary distance values in turn (essentially assumed to be exactly known for simplicity) versus the experimentally derived distance and its DPI derived sigma (L).
Greetings,
John
Prof John R Helliwell DSc
On 16 Dec 2011, at 16:07, John R Helliwell wrote:
> Dear Bie Gao,
> You can obtain an estimate of the standard deviation on your putative
> Mg to ligand distance using the diffraction precision index (DPI)
> approach of Cruickshank and Blow (1999 and 2002 Acta Cryst D). ie:-
> D M Blow Acta Cryst. (2002). D58, 792-797
> Synopsis: The formulae for the diffraction-component precision index
> introduced by Cruickshank [(1999), Acta Cryst. D55, 583-601] are
> simplifed using two approximations. A rearranged formula for the
> precision index is presented which can readily be calculated from
> experimental data.
>
>
> Using this you can add a quantitative test of statistical significance
> to the, of course, very senible earlier inputs to your questions. Do
> note though that the DPI is calculated as a number for the position
> error, sigma (x), on an atom with an average B factor. You have to
> adjust your DPI value for the atoms in question via the square root of
> their B value ratioed to the average B. For example a lower than
> average B gives a more precise sigma (x) than the average. Finally the
> sigma on the bond distance itself is calculated from the sigma (x)
> pair of values for each atom via the quadrature formula. The usual
> statistical test of significance is if the ligand distance (L) is then
>> 3sigma (L).
>
> Best wishes,
> Prof John R Helliwell DSc.
>
> On Thu, Dec 15, 2011 at 9:29 PM, bie gao wrote:
>> Thank you all for the help. These are the key factors I collected so far:
>> 1. Distance, Mg--O is shorter (2.0 -- 2.4A)
>> 2. Coordination, Mg is octahedrally coordinated.
>> 3. B factors, local B factors (i.e. the residues that coordinate with the
>> ion) should be similar.
>> 4. Use Mn++ to replace Mg.
>> I will look into these more.
>>
>> Best,
>> Gao
>>
>>
>> On Wed, Dec 14, 2011 at 5:45 PM, bie gao wrote:
>>>
>>> Hi every,
>>>
>>> I'm working with 2 crystal forms of a protein from 2 different
>>> crystallization conditions. Condition 1 has 100mM MgCl2. Condition 2
>>> doesn't. Both are ~2.9 angstrom. The 2 structures are virtually identical
>>> except in condition1, there is a clear positive density surrounded by a Glu
>>> side chain carboxyl and a couple of main carboxyl groups. (Again, condition
>>> 2 doesn't have this density).
>>>
>>> My initial thought is that a Mg atom is incorporated and it fits well. But
>>> the problem is we can not role out the possibility of a water molecule.
>>> Refining with Mg gives a b-factor of 42 (about average for the whole
>>> protein). The b-factor is 21 when refining with a water. Both cases there is
>>> no positive/negative density at contour=2.0.
>>>
>>> Based on the current data, is there any other role we can apply to see how
>>> likely it is a Mg or water. Or anomalous scattering is the only way? Thanks
>>> for your suggestions.
>>>
>>> Best,
>>> Gao
>>
>>
>
>
>
> --
> Professor John R Helliwell DSc
----------
From: Yuri Pompeu
In my personal opinion, whatever that is worth, I would question why you are modelling a Mg2+ ion if you are having to go through some trouble to prove it is there. If you dont see octahedral coordination to waters and or Asp/Glu it probably is not a Mg.
HTH
No comments:
Post a Comment