Well , maybe they are there (hydrogens), maybe they are not (also depends on location). They, or something else also boils sometimes. I also understand from some other publications such as doi:10.1107/S090904509002192 (cyclosporine) that hydrogen abstraction is irreversible. Is it supported my Mass Spectroscopy post mortem in the case of cyclosporine and aldose reductase? Just what left from the irradiated crystals - molecules with or without hydrogens can be checked in mass-spectrometer. BTW, part of my early life I practiced small molecule X-ray crystallography, which is by definition ultra-high resolution. When we wished to know in critical cases were hydrogens are and if they are, we exchanged them with deuterium in large crystals and performed neutron diffraction. One major advantage of neutron diffraction over X-ray diffraction is that the latter is rather insensitive to the presence of hydrogen (H) in a structure, whereas the nuclei 1H and 2H (i.e. Deuterium, D) are strong scatterers for neutrons. This means that the position of deuterium in a crystal structure and its thermal motions can be determined far more precisely with neutrons
Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 16, 2010, at 15:45 , Sanishvili, Ruslan wrote: > Hi Pavel, > > Note that in the ultra-high resolution structure of aldose reductase > http://www.ncbi.nlm.nih.gov/pubmed/15146478 > we didn't see all (or most) hydrogens. So, the converse question one could > ask is why we didn't see all of them? Was it only because of higher B-factors > or because some of them were stripped during data collection? > > Note that in my original message I said "they are, in most cases, still > assumed". Ultra-high resolution structures are exactly what I meant under few > cases when some of the positions are not assumed, so thanks for pointing that > out. > > It's not all or nothing - some hydrogens will be stripped and some won't. But > since we don't know which ones are gone, depositing the coordinates of all of > them may be misleading. It can be particularly dangerous for structure-based > functional interpretations because several publications suggest that active > sites are one of the first ones to suffer from radiation damage. And aren't > the functional interpretations the ultimate goal of protein structures? > > Cheers, > N. > > ________________________________ > > From: Pavel Afonine [mailto:pafon...@lbl.gov] > Sent: Wed 9/15/2010 5:56 PM > To: Sanishvili, Ruslan > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Deposition of riding H > > > > Hi Nukri, > > thanks for the paper (I haven't read the paper yet), I definitely missed > this one! > > Interesting though, if we assume that they get stripped off during data > collection, how you could see so many hydrogen atoms in Fo-Fc residual > maps for Aldose Reductase structure at 0.66A? > > B. Guillot, C. Jelsch, N. Muzet, C. Lecomte, E. Howard, B. > Chevrier, A. Mitschler, A. Podjarny, A. Cousson, R. Sanishvili & A. > Joachimiak (2000). Multipolar refinement of aldose reductase at > subatomic resolution. Acta Cryst. A56, s199. > > E. I. Howard, R. Cachau, A. Mitschler, P. Barth, B. Chevrier, V. > Lamour, A. Joachimiak, R. Sanishvili, M. Van Zandt, D. Moras & A. > Podjarny (2000). Crystallization of Aldose Reductase leading to Single > Wavelength (0.66 Å) and MAD (0.9 Å) subatomic resolution studies. Acta > Cryst. A56, s57. > > A. D. Podjarny, A. Mitschler, I. Hazemann, T. Petrova, F. Ruiz, E. > Howard, C. Darmanin, R. Chung, T. R. Schneider, R. Sanishvili, C. > Schulze-Briesse, T. Tomizaki, M. Van Zandt, M. Oka, A. Joachimiak & O. > El-Kabbani (2005). Inhibitor binding to aldose reductase studied at > subatomic resolution. Acta Cryst. A61, c122. > > Pavel. > > > On 9/15/10 3:34 PM, Sanishvili, Ruslan wrote: >> Hi All, >> >> I have not read all messages in the trace so my apologies if somebody >> already pointed out what I have to say. >> >> There is lot of talk about how this or that software treats the riding >> hydrogens. What to do with the fact that however these hydrogens are >> treated in calculations, they are, in most cases, still assumed? Meents >> et al http://scripts.iucr.org/cgi-bin/paper?xh0004 showed that proteins >> are stripped of hydrogens during X-ray data collection. So, IMHO it is a >> good argument against depositing the H coordinates in PDB. >> Cheers, >> N. >> >> >> Ruslan Sanishvili (Nukri), Ph.D. >> >> GM/CA-CAT >> Biosciences Division, ANL >> 9700 S. Cass Ave. >> Argonne, IL 60439 >> >> Tel: (630)252-0665 >> Fax: (630)252-0667 >> rsanishv...@anl.gov >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of >> George M. Sheldrick >> Sent: Wednesday, September 15, 2010 5:14 PM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Deposition of riding H >> >> Pavel: In my original email I very carefully gave credit for >> IMPLEMENTING the TLS concept. Of course the ideas and some >> programs had been around long before, but it was the >> IMPLEMENTATION IN REFMAC that resulted in TLS becoming >> widely used. I had actually considered putting it into SHELXL >> but had not done so for two reasons (a) I was too lazy and >> (b) I missed an essential trick that REFMAC introduced, namely >> the combination of TLS with an additive isotropic B-value for >> each atom. >> >> Dale: You are quite correct that AFIX 137 breaks my argument >> about not depositing (SHELX) hydrogen atoms because they can >> be recalculated with no loss of experimental information. >> However to be fair, if you generate the first .ins file using >> SHELXPRO (the recommended procedure) you will get AFIX 33 >> that doesn't have this problem. For Pavel and others unfamiliar >> with SHELXL, AFIX 33 is a pure riding model with a staggered >> methyl group but AFIX 137 assumes local threefold symmetry, >> finds the initial torsion angle by a three-fold averaged fit >> to the difference density and then refines the torsion angle >> in the following cycles. Since this torsion angle is not >> given explicitly in the output files, if AFIX 137 hydrogens >> are not deposited, they cannot be regenerated except by a full >> refinement against the experimental data. >> >> 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 Wed, 15 Sep 2010, George M. Sheldrick wrote: >> >>> Dear Pavel, >>> >>> May I suggest that you take a look at the SHELX manual: >>> http://shelx.uni-ac.gwdg.de/SHELX/shelx.pdf >>> before sending your SHELX questions to CCP4bb? You might >>> even find some good ideas for implementing in phenix_refine! >>> >>> For example, >>> if you look up 'non-crystallographic symmetry' in the index >>> you will discover that SHELXL applies NCS in the form of >>> restraints, not constraints, which has the advantage that it >>> can be applied locally and in combination with all other >>> restraints and constraints involving the same atoms. However >>> you will not find TLS in the index, because the credit for >>> implementing this very useful concept should be given to >>> Martin Winn, Garib and Ethan, long after the current version >>> of SHELXL (and its manual) were released in 1997. And because >>> SHELXL only reads one instruction file (*.ins) and one >>> reflection file (*.hkl) but no other data files or libraries, >>> and FORTRAN will always be FORTRAN, the deposition of these >>> two files would be sufficient to define the refinement for >>> posterity. >>> >>> Best wishes, 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 Wed, 15 Sep 2010, Pavel Afonine wrote: >>> >>>> Dear Felix, >>>> >>>>> Shortly Shelxl knows crystallography best. >>>> I have no doubts about this. May questions were, though: >>>> >>>>>> - how .ins file encodes the information about NCS groups used in >>>>>> refinement (atom selection for NCS groups, restraint weights for >> different >>>>>> groups, etc? >>>>>> >>>>>> - how .ins file encodes the information about TLS (again, atom >> selections >>>>>> for TLS groups, TLS matrices, etc)? Related, does it have a >> concept of >>>>>> having TLS and other components to the total atomic displacement >> parameter >>>>>> (ADP)? >>>>>> >>>>>> - If I recall it correctly, to fix (=not refine) a certain >> parameter (say >>>>>> occupancy or B-factor) in Shelxl you need to add a number 10 to >> it. Is it >>>>>> true? IMHO, this might lead to confusion if such a file gets >> deposited to >>>>>> PDB. >>>> Best, >>>> Pavel. >>>> >>>> >>>
