Dear Sir,
That is true the ligand is ATP, the occupancy problem
comes only for the phosphates. This ATP tends to get
cleaved to ADP and AMP in other complexes I got. So in
this case do you suggest keeping different occupancies
for nucleoside and phosphate groups? I am not aware of
any publication with this scenario so I am not sure whether
it is right.
Thank you
Regards
Kavya
> Dear Kavyashree,
>
> It is possible that your bound ligand (for which you have strong electron
> density) is actually a break-down of the parent compound? We have seen
> this a couple of times now.
>
> Also - are the poorly refining areas (those with negative density) part of
> a pendant ring connected by a conformationally unrestricted bond? These
> quite often have poor density.
>
> Hard to judge without seeing the actual density - but understand why!
>
> Regards,
> Antony.
>
>
> Sent from my iPhone
>
> On 25 May 2013, at 10:40, "Kavyashree Manjunath" <[log in to unmask]>
> wrote:
>
>> Dear Sir,
>>
>> Thank you all for your kind advice and clarifications.
>> I will keep the occupancy 1.0 for both the ligands and
>> refine without considering the negative density in this
>> case.
>>
>> Thanking you
>> Regards
>> Kavya
>>
>>
>>
>>> -----BEGIN PGP SIGNED MESSAGE-----
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>>>
>>> Dear Kavya,
>>>
>>> I don't see much sense in having different occupancies within the same
>>> molecule (unless one atoms sits on a special position, but then refmac
>>> will take care of it).
>>>
>>> If positive density comes up it's a good sign the ligand really is
>>> there. At 2.2A I would not be too surprised some atoms show less
>>> density than others (but don't look too much at the map with a sigma
>>> level < 1: you are going to see what you want to see).
>>>
>>> It's difficult to judge without sitting next to you, so my advice is
>>> try to model it as good as your knowledge permits, and do take your
>>> chemical knowledge into account when doing so!
>>>
>>> Best,
>>> Tim
>>>
>>> On 05/25/2013 06:55 AM, Kavyashree Manjunath wrote:
>>>> Dear users,
>>>>
>>>> I tried giving occupancy of 0.65 and 0.6 respectively for all atoms
>>>> of the two ligands and refined. Now after refinement, the atoms of
>>>> ligand does not have negative density but those which did not have
>>>> negative density previously appear positive. So what do I need to
>>>> do? under what circumstances does a ligand have different
>>>> occupancies for different atoms or for a group of atoms. Any such
>>>> references are very much welcome.
>>>>
>>>> Thank you Regards Kavya
>>>>
>>>>> Sir,
>>>>>
>>>>> Yes it is around ligand. The average B-factor of one of the
>>>>> ligand is 36.78, of which one of the atom has occupancy B
>>>>> factor 0.58 39.37 0.56 38.77 0.87
>>>>> 37.00 Three atoms are of same type. The other ligand's overall
>>>>> Bfactor is 17.64. occupancy B factor 1.00 19.29
>>>>> 0.64 23.90 Two atoms are of same type.
>>>>>
>>>>> So in the present case should I put the occupancy of 0.56 for all
>>>>> atoms of ligand-1 and 0.64 for all atoms of ligand-2 and refine?
>>>>>
>>>>> I mean will it be wrong to put different occupancies for
>>>>> different atoms of same ligand?
>>>>>
>>>>> I could not see any alternate densities coming up for those
>>>>> atoms which did not have densities. But 2FoFc map would appear
>>>>> around these atoms at 0.7 sigma at the same position where the
>>>>> atoms are present.
>>>>>
>>>>> Thank you Regards Kavya
>>>>>
>>>>>> Hi Kavya,
>>>>>>
>>>>>> If I understand you correctly (from title and text), you meant
>>>>>> your negative FoFc was around your ligand, is that right? I
>>>>>> wonder if this is a case in which the ligand has an occupancy
>>>>>> below 1, but was modeled as 1, so the refinement program had to
>>>>>> give it a high B factor to compensate that, which results in
>>>>>> the electron density bleeding into nearby space where there
>>>>>> should not be so much of it. If you want to test this
>>>>>> hypothesis, one thing you can try is to set the occupancy to
>>>>>> 0.25, 0.5,0.75 and so on, and refine a few cycles to see what
>>>>>> happens to the maps. Also, what's the B factor of the ligand,
>>>>>> and what's the B of the nearby protein atoms? The difference
>>>>>> between them can also give you some hint for guessing the
>>>>>> ligand's occupancy. Some refinement programs(phenix.refine and
>>>>>> shelx) can also let you refine the ligand's occupancy.
>>>>>>
>>>>>> As to the "missing" atoms, that could be caused by alternative
>>>>>> conformations of the ligand - assuming you have already done a
>>>>>> thorough refinement.
>>>>>>
>>>>>> Zhijie
>>>>>>
>>>>>> -------------------------------------------------- From:
>>>>>> "Kavyashree Manjunath" <[log in to unmask]> Sent: Friday,
>>>>>> May 24, 2013 12:50 PM To: <[log in to unmask]> Subject:
>>>>>> [ccp4bb] Negative FoFc around ligand
>>>>>>
>>>>>>> Dear users,
>>>>>>>
>>>>>>> I am using refmac 5.7.0029 for refining a structure
>>>>>>> (resolution 2.2 Ang) bound to 2 ligands. After MR There is a
>>>>>>> very clear density of ligands but after refinement, I get
>>>>>>> negative fofc map near one of the ligand upto 5 sigma.
>>>>>>> However its 2fofc map covers the whole ligand. Also for the
>>>>>>> other ligand, I do not see any 2fofc density (at 3 sigma) for
>>>>>>> 2 atoms, without these atoms the ligand is unrealistic. But
>>>>>>> the density comes up around these at around 0.7 sigma.
>>>>>>> Overall completeness is 99.9% Rmerge 7.5%
>>>>>>>
>>>>>>> What else I need to check in the data. Kindly provide some
>>>>>>> suggestions.
>>>>>>>
>>>>>>> Thanking you Regards Kavya
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
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>>>>>
>>>>>
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>>> - --
>>> Dr Tim Gruene
>>> Institut fuer anorganische Chemie
>>> Tammannstr. 4
>>> D-37077 Goettingen
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