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" <[email protected]> > 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----- >>> Hash: SHA1 >>> >>> 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" <[email protected]> Sent: Friday, >>>>>> May 24, 2013 12:50 PM To: <[email protected]> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- This message has been scanned for viruses and dangerous >>>>>>> content by MailScanner, and is believed to be clean. >>>>>> >>>>>> >>>>>> -- This message has been scanned for viruses and dangerous >>>>>> content by MailScanner, and is believed to be clean. >>>>> >>>>> >>>>> >>>>> -- This message has been scanned for viruses and dangerous >>>>> content by MailScanner, and is believed to be clean. >>> >>> - -- >>> Dr Tim Gruene >>> Institut fuer anorganische Chemie >>> Tammannstr. 4 >>> D-37077 Goettingen >>> >>> GPG Key ID = A46BEE1A >>> -----BEGIN PGP SIGNATURE----- >>> Version: GnuPG v1.4.12 (GNU/Linux) >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >>> >>> iD8DBQFRoHp0UxlJ7aRr7hoRAti/AJ9PQQE8cgccPFuaWN842qlwkCK8FgCg/BPR >>> 8485l18SMJ4Th5XD0X5be1w= >>> =GfVo >>> -----END PGP SIGNATURE----- >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner, and is >>> believed to be clean. >> >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
