Re: [ccp4bb] largest protein crystal ever grown?
Hi Derek, That brings back memories. I am pretty certain that is the myoglobin crystal that was already on Benno's shelf at Brookhaven when I went there in 1980 to collect my oxymyoglobin neutron data. It would the metmyoglobin crystal Benno got the early neutron data from. He just kept it on the shelf because there was, of course, no degradation in the beam and a crystal is a pretty stable way to store a protein. Whenever he wanted more data he took it off the shelf and put it back on the beamline. If Benno is reading this bulletin board I am sure he could tell us more. Simon Simon E.V. Phillips Director, Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email: susan.jo...@rc-harwell.ac.uk Direct email: simon.phill...@rc-harwell.ac.uk Tel: +44 (0)1235 567701 (direct) +44 (0)1235 567700 (sec) +44 (0)7884 436011 (mobile) www: www.rc-harwell.ac.uk -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Derek Logan Sent: 24 October 2013 19:08 To: ccp4bb Subject: Re: [ccp4bb] largest protein crystal ever grown? Hi, Last spring I visited the Protein Crystallography Station at Los Alamos. On a shelf, in a capillary in a serious exhibition-quality glass dome, was a crystal of myoglobin some 50 mm**3, if I remember correctly. I was told it had been made by Benno Schoenborn some decades earlier and had been exposed to most of the neutron sources in the world (radiation damage - forget about it!) Paul Langan or Zoë Fisher can correct me if I've exaggerated the size or age. Anyway, as I already lost the record several times over for having seen the biggest protein crystal ever, I can share with you the surprise and delight of having to centre the crystals using a telescope mounted on a tripod on the other side of the room. Apparently the magnification on the microscope on the diffractometer (visible in this photo, and maybe the giant crystal too? http://www.lanl.gov/_assets/php/flickrImage.php?photo_id=5033219363secret=291f519124) was too high, so any neutron-size crystals would filled the whole field of view even if they were not well-centered. FWIW, my crystals (somewhat optimistically 0.4 mm**3) didn't diffract neutrons even after a 24h exposure :-) Derek Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se Centre for Molecular Protein Science www.maxlab.lu.se/node/307 Lund University, Box 124, 221 00 Lund, Sweden On 24 Oct 2013, at 18:35, Victor Lamzin vic...@embl-hamburg.de wrote: Also following on from John's comment - back to the times of my PhD I was repeatedly growing crystals of bacterial formate dehydrogenase (80 kDa) of a size about 7x1.5x1 mm. I thought that was quite normal and did not even think of making a photo of 'just a protein crystal'. Victor This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
Re: [ccp4bb] largest protein crystal ever grown?
I once grew an oxymyoglobin crystal 1 cm long for neutron diffraction at Brookhaven. I was very proud of it, but when I got to Brookhaven I was told it was too big for the beam (!) so I had to use a much smaller one of only 8 mm**3 (Nature 292:81-82 (1981). I still have a few left over that look like 5-7 mm long (I just held a ruler up to the tube which is still on my office shelf) Simon E.V. Phillips Director, Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email: susan.jo...@rc-harwell.ac.ukmailto:susan.jo...@rc-harwell.ac.uk Direct email: simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@rc-harwell.ac.uk Tel: +44 (0)1235 567701 (direct) +44 (0)1235 567700 (sec) +44 (0)7884 436011 (mobile) www: www.rc-harwell.ac.ukhttp://www.rc-harwell.ac.uk/ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tobias Beck Sent: 24 October 2013 16:34 To: ccp4bb Subject: [ccp4bb] largest protein crystal ever grown? Dear all, I was just wondering if anyone has some information or references about the dimensions of the largest protein crystal ever grown? I am aware that for neutron protein crystallography one usually needs crystals with mm dimensions. I have found some information on crystallization under micro-gravity and how this can enlarge the crystal size. However, I would rather be interested in the dimensions for crystals obtained from a regular lab setup. Thanks, Tobias. -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___ This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
[ccp4bb] Postdoctoral posts as RCaH and Oxford
FIVE POSTDOCTORAL POSTS IN STRUCTURAL AND MOLECULAR BIOLOGY: RESEARCH COMPLEX AT HARWELL (RCAH) AND WEATHERALL INSTITUTE OF MOLECULAR MEDICINE (WIMM) WITH DEPARTMENT OF CHEMISTRY, UNIVERSITY OF OXFORD. Applications are invited for Postdoctoral Scientists (posts 1-3) for three years in an exciting new research programme to discover and develop small molecule inhibitors of mutant RAS for treatment of cancer. This new chemical biology drug discovery programme has co-investigators based at the Weatherall Institute of Molecular Medicine, the Research Complex at Harwell (RCaH) and the Department of Chemistry, Oxford, and is funded by the Wellcome Trust Seeding Drug Discovery Initiative. The aim of the project is to discover small-molecule drugs that inhibit protein-protein interactions involving the RAS family of proteins for treatment of cancer. The project will adopt a highly innovative strategy using single domain antibody fragments as tools for identification of drug-like molecules. Post 1 is for a structural biologist with a PhD in structural biology. Experience with solving structures using X-ray diffraction, crystallography of protein-ligand complexes, co-crystallisation and crystal soaking methods are essential. Experience with surface plasmon resonance and small molecule library screening will be advantageous. The post will be based in the laboratory of Professor Simon Phillips http://www.rc-harwell.ac.uk/directors.html at RCaH (adjacent to the Diamond Synchrotron). Informal enquiries may be made by email to simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@rc-harwell.ac.uk and terence.rabbi...@imm.ox.ac.ukmailto:terence.rabbi...@imm.ox.ac.uk. Applications for this vacancy are to be made online. To apply for this role and for further details, including a job description and selection criteria, please use:- https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106083 The closing date for this position is noon on Friday 08 March 2013. Please quote reference 106083. Posts 2 and 3 are suitable for molecular biologists with a PhD in molecular biology. Experience with recombinant protein production and purification, DNA transfection of mammalian cells, complex genetic engineering and site directed mutagenesis are essential. Experience with signal transduction cell biology, small molecule library screening and structural biology will be advantageous. The posts will be based in the laboratory of Professor Terry Rabbitts http://www.imm.ox.ac.uk/wimm-research/molhaem/terry_rabbitts at the Weatherall Institute of Molecular Medicine. Informal enquiries may be made by email to terence.rabbi...@imm.ox.ac.ukmailto:terence.rabbi...@imm.ox.ac.uk. Applications online at: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106082 The closing date for these positions is midday on Friday 08 March 2013. Please quote reference 106082. Applications are also invited for two postdoctoral positions (Posts 4 and 5) in a new programme, funded by Leukaemia and Lymphoma Research, to discover and develop small molecule inhibitors of oncogenic proteins for the treatment of leukaemia/lymphoma. The posts will be available for 3 years in the laboratory of Professor Terry Rabbitts http://www.imm.ox.ac.uk/wimm-research/molhaem/terry_rabbitts. The aim of this project is to discover small-molecule drugs that inhibit protein-protein interactions involving transcription factor multi-protein complexes in leukaemia and lymphoma. The approach will involve novel strategies using single domain antibody fragments and peptide aptamers, as tools for the identification of drug-like molecules to lead the development for treatment of cancer. The programme involves structural determination of leukaemia proteins together with screening and characterization of small molecule inhibitors of protein-protein interactions. In particular, the project will use the structure of single antibody domains as templates for drug lead development. Posts 4 and 5 are for molecular biologists with a PhD in structural biology, experience with recombinant protein production purification and with solving structures using X-ray diffraction. Experience with surface plasmon resonance, AlphaScreen and other methods for small molecule screening and NMR are desirable. Informal enquiries may be made to Professor Terry Rabbitts at terence.rabbi...@imm.ox.ac.ukmailto:terence.rabbi...@imm.ox.ac.uk. Applications online at: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106000 The closing date for these positions is noon on Friday 08 February 2013. Please quote reference 106000.
Re: [ccp4bb] I/sigmaI of 3.0 rule
I take the point about a tendency in those days to apply sigma cutoffs to get lower R values, which were erroneously expected to indicate better structures. I wonder how many of us remember this paper by Arnberg et al (1979) Acta Cryst A35, 497-499, where it is shown for (small molecule) structures that had been refined with only reflections I3*sigma(I) that the models were degraded by leaving out weak data (although the R factors looked better of course). Arnberg et al took published structures and showed the refined models got better when the weak data were included. The best bit, I think, was when they went on to demonstrate successful refinement of a structure using ONLY the weak data where I3*sigma(I) and ignoring all the strong ones. This shows, as was alluded to earlier in the discussion, that a weak reflection puts a powerful constraint on a refinement, especially if there are other stronger reflections in the same resolution range. --- | Simon E.V. Phillips | --- | Director, Research Complex at Harwell (RCaH)| | Rutherford Appleton Laboratory | | Harwell Science and Innovation Campus | | Didcot | | Oxon OX11 0FA | | United Kingdom | | Email: simon.phill...@rc-harwell.ac.uk | | Tel: +44 (0)1235 567701 | |+44 (0)1235 567700 (sec) | |+44 (0)7884 436011 (mobile) | | www.rc-harwell.ac.uk| --- | Astbury Centre for Structural Molecular Biology | | Institute of Molecular and Cellular Biology | | University of LEEDS | | LEEDS LS2 9JT | | United Kingdom | | Email: s.e.v.phill...@leeds.ac.uk | | Tel: +44 (0)113 343 3027 | | WWW: http://www.astbury.leeds.ac.uk/People/staffpage.php?StaffID=SEVP | ---
[ccp4bb] FW: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]
Dear Tim, Interesting discussion, and I agree with your last description of the issues. When I started playing with this for oxymyoglobin [J. Mol. Biol. 142, 531-544 (1980)] it seemed immediately apparent (i.e. by thinking about it before starting to write programs) that the simple Babinet approach was deficient since the solvent was not just the inverse of the protein. This is Tim's point about not using Fc in the Babinet method because protein density is not flat (but you could use a flat protein model Fm). As pointed out in this discussion, there is not much difference between the two at 20A resolution anyway, but what did become apparent when I started doing actual calculations was that the solvent effect was noticeable even at moderate resolutions. It seemed to me then that the obvious was to go was a flat solvent to generate Fs. The issues then were where to put the protein-solvent boundary, and how sharp to make it (i.e. a B factor). I also noticed that when the mask was made, small cavities in the protein would generate bits of solvent in the interior of the protein that should not be there (another issue alluded to in the discussion). In those days I was looking at maps/masks plotted on paper rather than graphics, and I solved the cavity problem manually by adding atoms in the cavities in the pdb file I used to make the mask until I couldn't see any more cavities left in a plot. This is not, of course, an automatic procedure, and that would need a bit of thought. The determination of the border width between protein and solvent, and the B factor, were just optimised by trial and error, running several values, plotting R factors and fitting a function to them (parabola I think) to help find a minimum. Again the issue for automating this requires finding suitable parameters with derivatives. Having done all this in a simple-minded way, I was very impressed by the effect on the refinement, and on of the figures in the JMB paper shows how dramatic it was and how far up the resolution range the effect was felt. At this stage I should have programmed it properly, but the oxymyglobin structure was done, I had to move jobs and projects and good intentions fell by the wayside (mea culpa). Luckily more public spirited people picked up some of the ideas and improved them, but the protein cavity issue is still there it seems. Obviously I would like to add my vote for a proper flat (or nearly?) solvent mask model as being the right apporach. Simon --- | Simon E.V. Phillips | --- | Director, Research Complex at Harwell (RCaH)| | Rutherford Appleton Laboratory | | Harwell Science and Innovation Campus | | Didcot | | Oxon OX11 0FA | | United Kingdom | | Email: simon.phill...@rc-harwell.ac.uk | | Tel: +44 (0)1235 567701 | |+44 (0)1235 567700 (sec) | |+44 (0)7884 436011 (mobile) | | www.rc-harwell.ac.uk| --- | Astbury Centre for Structural Molecular Biology | | Institute of Molecular and Cellular Biology | | University of LEEDS | | LEEDS LS2 9JT | | United Kingdom | | Email: s.e.v.phill...@leeds.ac.uk | | Tel: +44 (0)113 343 3027 | | WWW: http://www.astbury.leeds.ac.uk/People/staffpage.php?StaffID=SEVP | --- -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Fenn Sent: 23 October 2010 21:14 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem] On Sat, 23 Oct 2010 10:05:15 -0700 Pavel Afonine pafon...@gmail.com wrote: Hi Tim, ...but I hope this answers the question: Babinet's vs. the flat model? Use them together! ;) thanks a lot for your reply. Could you please explain the *physical* meaning of using both models together? I can try! Typically, we model the bulk solvent using a real space mask that is set to 1 in
Re: [ccp4bb] units of f0, f', f''
Dear CCP4BBers, I believe the answer to this question is that the correct unit for the scattering factor is actually length (the square root of the scattering cross section), i.e. it is strictly the scattering length. In the dim and distant past I did some neutron diffraction, and scattering factors here are typically expressed in cm (not very SI I know). In ND the factors vary oddly with atomic number so you have to use the correct units. In X-ray diffraction it goes with the number of electrons (which are all the same after all) so it was convenient to define scattering factors as a ratio by dividing by the scattering length of hydrogen, so f for hydrogen (i.e. one electron) becomes one, rather than a length in cm. f, f' etc. then become dimensionless quantities, and the maps come out effectively in e/A**2 (whereas they are really in scattering density). In ND, of course, you cannot do this and the maps are in units of scattering density. Simon Phillips --- | Simon E.V. Phillips | --- | Director, Research Complex at Harwell (RCaH)| | Diamond Light Source Ltd| | Diamond House | | Chilton | | Didcot | | Oxon OX11 0DE | | United Kingdom | | Email: simon.phill...@diamond.ac.uk | | Tel: +44 (0)1235 778946 | |+44 (0)1235 778431 (sec) | |+44 (0)7884 436011 (mobile) | | www.mrc.ac.uk/OurResearch/ResourcesforScientists/ResearchComplex| --- | Astbury Centre for Structural Molecular Biology | | Institute of Molecular and Cellular Biology | | University of LEEDS | | LEEDS LS2 9JT | | United Kingdom | | Email: s.e.v.phill...@leeds.ac.uk | | Tel: +44 (0)113 343 3027 | | WWW: http://www.astbury.leeds.ac.uk/People/staffpage.php?StaffID=SEVP | --- -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: 26 February 2010 08:46 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] units of f0, f', f'' Depends on in what units you want to get your electron density in, or what scattering objects (electrons) you integrate over for the SF formula. Since the exponent is dimensionless in the SF formula, and the FT commonly is electron density, electrons (not negative charge) has to be somewhere in the SF formula. If fo is in electrons, then f' and f have to be units of electrons as well. The f' component reduces the real part scattering, it is negative (in electron units, again not in charge). BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Thursday, February 25, 2010 11:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] units of f0, f', f'' Dear all, I just stumbled across the question about what is the unit of f' and f''. The first couple of hits from ixquick.com claim it was e^-. Since e^- is not a unit but symbolises an elemtary particle (of which fractions are considered non-existent), I was wondering whether the unit of f, f', and f'' is actually e (a positive charge!) and the value of f^0 of Fe at its K-edge was actually 26e or -26e - see e.g. Table 1 in http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Post-doctoral positions (x2) in Protein Crystallography at the Research Complex at Harwell
Post-doctoral positions (x2) in Protein Crystallography Research Complex at Harwell (RCaH) We have two postdoctoral positions available for protein crystallographers at the Research Complex at Harwell (RCaH), a new laboratory currently nearing completion adjacent to the UK Diamond synchrotron. The positions are funded by a five-year MRC research grant to Simon Phillips and Steve Carr to work on structural studies of complexes involved in Holliday junction resolution. RCaH will be equipped to a high standard for structural biology, and will also house the Oxford Protein Production Facility UK (OPPF-UK), the CCP4 core team, membrane protein crystallography groups of So Iwata and Alex Cameron, as well as other multidisciplinary groups in life and physical sciences. You should have a PhD in a relevant subject and experience in protein crystallography. Further information is available at the RCaH website (www.rc-harwell.ac.uk), and for informal enquiries please email: stephen.c...@rc-harwell.ac.uk Applications for this role must be made online at http://jobs.mrc.ac.uk inputting reference RCH09/589. If you do not have internet access or experience technical difficulties please call 01793 301156. Closing date 1st January 2010 For further information about the MRC please visit www.mrc.ac.uk. The Medical Research Council is an Equal Opportunities Employer --- | Simon E.V. Phillips | --- Director, Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Science and Innovation Campus Didcot Oxon OX11 0FA United Kingdom Email: rhian.mor...@rc-harwell.ac.ukmailto:r...@diamond.ac.uk Direct email: simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@diamond.ac.uk Tel: +44 (0)1235 567701 (direct) +44 (0)1235 567700 (sec) +44 (0)7884 436011 (mobile) www: www.rc-harwell.ac.uk Visiting Professor of Biophysics Astbury Centre for Structural Molecular Biology University of Leeds Visiting Professor in Molecular Biophysics Department of Biochemistry University of Oxford This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
[ccp4bb] Post-doctoral positions (x2) in Protein Crystallography
Post-doctoral positions (x2) in Protein Crystallography Research Complex at Harwell (RCaH) We have two postdoctoral positions available for protein crystallographers at the Research Complex at Harwell (RCaH), a new laboratory currently nearing completion adjacent to the UK Diamond synchrotron. The positions are funded by a five-year MRC research grant to Simon Phillips and Steve Carr to work on structural studies of complexes involved in Holliday junction resolution. RCaH will be equipped to a high standard for structural biology, and will also house the Oxford Protein Production Facility UK (OPPF-UK), the CCP4 core team, membrane protein crystallography groups of So Iwata and Alex Cameron, as well as other multidisciplinary groups in life and physical sciences. You should have a PhD in a relevant subject and experience in protein crystallography. Further information is available at the RCaH website (www.rc-harwell.ac.uk), and for informal enquiries please email: stephen.c...@rc-harwell.ac.uk Applications for this role must be made online at http://jobs.mrc.ac.uk inputting reference RCH09/589. If you do not have internet access or experience technical difficulties please call 01793 301156. Closing date 1st January 2010 For further information about the MRC please visit www.mrc.ac.uk. The Medical Research Council is an Equal Opportunities Employer --- | Simon E.V. Phillips | --- Director, Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Science and Innovation Campus Didcot Oxon OX11 0FA United Kingdom Email: rhian.mor...@rc-harwell.ac.uk Direct email: simon.phill...@rc-harwell.ac.uk
[ccp4bb] MRC Grant Opportunities the Research Complex at Harwell (not relevant to non-UK CCP4BBers)
Dear CCP4BBers, With apologies to non-UK crystallographers (to whom it is not relevant so they should read no further). Just to let you know that there are opportunities for grant and fellowship applications from researchers wishing to work in the Research Complex at Harwell (RCaH). This is a great new lab being built next door to Diamond, which is a prime spot for PX since it will also house the CCP4 core team and the Oxford Protein Production Facility (OPPF). A call has just gone out from MRC, and the other Research Councils have/will have schemes (e.g. the BBSRC Diamond Fellowship scheme, which is closing soon, but there will be other calls). Full information of the MRC calls can be found on the website: http://www.mrc.ac.uk/ApplyingforaGrant/CallsForProposals/RCaH/index.htm. General info on RCaH on www.mrc.ac.uk/OurResearch/ResourcesforScientists/ResearchComplex --- | Simon E.V. Phillips | --- Director, Research Complex at Harwell (RCaH) Diamond Light Source Ltd Diamond House Chilton Didcot Oxon OX11 0DE United Kingdom Email: [EMAIL PROTECTED] Tel: +44 (0)1235 778946 +44 (0)1235 778431 (sec) +44 (0)7884 436011 (mobile) www: www.mrc.ac.uk/OurResearch/ResourcesforScientists/ResearchComplex Visiting Professor of Biophysics Astbury Centre for Structural Molecular Biology University of Leeds Visiting Professor in Molecular Biophysics Department of Biochemistry University of Oxford
