[ccp4bb] Electron density server
Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan
Re: [ccp4bb] Electron density server
Dear Rojan, Get the mmCIF, then use CIF2MTZ from CCP4. Cheers, Clement On 10/25/13 3:07 PM, Rojan Shrestha wrote: Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan
Re: [ccp4bb] largest protein crystal ever grown?
Dear all, dear John, Thanks for the replies and references! I like the ice cream tub setup. Best wishes, Tobias. On Thu, Oct 24, 2013 at 10:05 PM, Jrh jrhelliw...@gmail.com wrote: Dear Tobias, There is also this one :- http://dx.doi.org/10.1107/S0021889801007245 In this study we had to use a smaller crystal than the largest ones available of 125mm3. They were a lovely rhombic dodecahedral crystal habit. Nb we only published details of the size of the one used. These crystals were grown by Joseph Gilboa at The Weizmann Institute, who we miss dearly. See the appreciation of Joseph by Felix Frolow and myself at http://dx.doi.org/10.1107/S0021889810006941 Yours sincerely, John Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol. Chair School of Chemistry, University of Manchester, Athena Swan Team. http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html On 24 Oct 2013, at 16:33, Tobias Beck tobiasb...@gmail.com wrote: 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 ___ -- ___ 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 ___
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.
[ccp4bb] Tool to compute F/FP from F(+) / F(-)
Hello, What is the tool in CCP4 to calculate F from F(+) and F(-) with their standard deviations? Regards, Rojan
Re: [ccp4bb] strange unit cell
You could try putting this into the Zanuda server http://www.ysbl.york.ac.uk/YSBLPrograms/ which will search for possible correct spacegroups given the coordinates and structure factors. There are however no reasons why you can't have a pseudo-cubic monoclinic lattice, however unlikely it is. Best wishes, Graeme On 25 October 2013 01:55, 유상헌 s...@snu.ac.kr wrote: Hi everyone, ** ** Recently I’ve got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn’t do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? ** ** Thanks, ** ** Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA ** ** ** **
[ccp4bb] AW: [ccp4bb] strange unit cell
Dear Sangheon, there is no law that forbids P21 crystals to have a~b~c and beta~90°. It only does not happen very often. So your solution can be correct. You may want to analyze your crystal packing with ccp4 program Zanuda, to see if a higher symmetry space group could be used. Best regards, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ??? Gesendet: Freitag, 25. Oktober 2013 02:56 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] strange unit cell Hi everyone, Recently I've got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I'm confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn't do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? Thanks, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
[ccp4bb] Deadline looming for Travel bursaries for CCP4 Study Weekend 2014
The deadline for applications for travel bursaries for students and young post-docs from non-UK laboratories to help them to attend the CCP4 Study Weekend is drawing close. A reminder all applications must be received by 31st October 2013. More details (taken from Study Weekend website) are detailed below. TRAVEL BURSARIES Limited funds will also be made available to help pay travel costs for students and young post-docs from non-UK laboratories. Please send a separate letter, signed by your supervisor and stating the expected cost of travel in pounds sterling, to justify applications for travel support. Supervisors are asked to nominate only one candidate from their Laboratory. Delegates are expected to travel by the most economic means possible. Candidates from less favoured regions will be given preference. Applications should be sent to... Carol Malpass CCP4 Study Weekend Travel Bursary Science and Technology Facilities Council Rutherford Appleton Laboratory RCaH 1.22 Harwell Oxford Didcot OX11 0FA, UK You can also fax copies of your letters to Carol on +44 (0)1235 567720 or e-mail carol.malp...@stfc.ac.ukmailto:carol.malp...@stfc.ac.uk. Applications for Travel Assistance MUST be received by 31 October 2013 -- Scanned by iCritical.
Re: [ccp4bb] Tool to compute F/FP from F(+) / F(-)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rojan, I would try aimless with the option 'onlymerge'. Best, Tim On 10/25/2013 09:33 AM, Rojan Shrestha wrote: Hello, What is the tool in CCP4 to calculate F from F(+) and F(-) with their standard deviations? Regards, Rojan - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSajG9UxlJ7aRr7hoRApvtAKDAUqTykSs06NhOAveRMIYQyeou9wCdH4YN E3/HNFgQlCCzYHfXcfzpxPs= =IOXY -END PGP SIGNATURE-
Re: [ccp4bb] Tool to compute F/FP from F(+) / F(-)
That won't work. Aimless expects intensities not Fs. I would think you could do it with sftools Phil On 25 Oct 2013, at 09:54, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rojan, I would try aimless with the option 'onlymerge'. Best, Tim On 10/25/2013 09:33 AM, Rojan Shrestha wrote: Hello, What is the tool in CCP4 to calculate F from F(+) and F(-) with their standard deviations? Regards, Rojan - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSajG9UxlJ7aRr7hoRApvtAKDAUqTykSs06NhOAveRMIYQyeou9wCdH4YN E3/HNFgQlCCzYHfXcfzpxPs= =IOXY -END PGP SIGNATURE-
[ccp4bb] השב: Re: [ccp4bb] largest protein crystal ever grown?
Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: 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] strange unit cell
Dear Sangheon, you don't say which cubic space group you tried, perhaps you tried the wrong one? Did Pointless indicate a clear preference? Between P23 and P213 for instance you can tell by systematic absences along h (if they were collected ok), but between I23 and I213 the only option is to try both and see if one or the other leads to a good solution. In any case, in principle having P21 with beta near 90 and a nearly equal to b and c is rare, but possible. Greetings, Mark Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 25 Oct 2013, at 02:55, 유상헌 wrote: Hi everyone, Recently I’ve got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn’t do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? Thanks, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
Re: [ccp4bb] strange unit cell
Hi Sangheon As others have said, there is nothing that stops a cell being monoclinic with those cell dimensions - indeed, there is nothing stopping it being triclinic, orthorhombic or tetragonal either (or even rhombohedral, for those of us who like to describe it with non-hexagonal axes). What *is* important is the symmetry of the reciprocal lattice; looking at projections of the reciprocal lattice along the major axes (i.e. a*, b* or c*) using a tool like hklview or viewhkl (both of which are in ccp4 6.4.0) should be sufficient to demonstrate whether you really have the higher symmetry. On 25 Oct 2013, at 01:55, 유상헌 wrote: Hi everyone, Recently I’ve got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn’t do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? Thanks, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] Postdoctoral position available @ EMBL-Hamburg, SAXS
Dear All, I would like to inform you that a postdoctoral position is available at the EMBL Hamburg Unit in the research group of Dmitri Svergun. I attach a brief description of the Vacancy Notice below. Deadline for application is 15th December 2013. Further Detailed Information can be found under : http://www.embl-hamburg.de/aboutus/jobs/searchjobs/index.php?newlang=1newms=srsearchregion=668 http://www.embl-hamburg.de/aboutus/jobs/searchjobs/index.php?newlang=1newms=srsearchregion=668 *Postdoctoral Positon, Reference HH_00053 * Applications are invited for a postdoctoral position in computational methods development for Biological SAXS in the BioSAXS group http://www.embl-hamburg.de/research/unit/svergun/index.html. The position is within BioStruct-X, an integrated project funded by Seventh Framework Programme (FP7) of the European Commission (www.biostruct-x.eu http://www.biostruct-x.eu). The successful candidate will participate in the design of an automated data analysis system to construct and validate 3D structural models from solution scattering data. The developments envisage hybrid applications of SAXS with other structural, biophysical and computational methods, including MX, NMR, electron microscopy and bioinformatic approaches.. The successful candidate will work on computational methods development for automated data analysis, storage and tracking, and on the cross-validation of SAXS models using the information from experimental techniques and also bioinformatic approaches. These developments are to be implemented at the high brilliance BioSAXS beamline of the EMBL at the Petra-III storage ring and also at the beamlines of the BioStruct-X partners. Regards Margret Fischer
Re: [ccp4bb] largest protein crystal ever grown?
Well if we start recalling rumours, I have heard that in UC San Diego in the laboratory of George Feher there was (is) a tetragonal hen egg white lysozyme crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. I have never visited George laboratory, but maybe among the society there are some who can shed some light on that…. FF 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 Oct 25, 2013, at 12:18 , Boaz Shaanan bshaa...@bgu.ac.il wrote: Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: 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
Re: [ccp4bb] largest protein crystal ever grown?
Hi Felix, What was the mosaicity of this crystal? The absorption correction must have been challenging too... Derek On 25 Oct 2013, at 13:23, Felix Frolow mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il wrote: Well if we start recalling rumours, I have heard that in UC San Diego in the laboratory of George Feher there was (is) a tetragonal hen egg white lysozyme crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. I have never visited George laboratory, but maybe among the society there are some who can shed some light on that…. FF 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.ilmailto:mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 25, 2013, at 12:18 , Boaz Shaanan bshaa...@bgu.ac.ilmailto:bshaa...@bgu.ac.il wrote: Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK נושא: 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.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/ -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.sehttp://www.cmps.lu.se/ Centre for Molecular Protein Science www.maxlab.lu.se/node/307http://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.demailto: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
Re: [ccp4bb] Tool to compute F/FP from F(+) / F(-)
Rojan Shrestha wrote: What is the tool in CCP4 to calculate F from F(+) and F(-) with their standard deviations? mtzMADmod
Re: [ccp4bb] largest protein crystal ever grown?
I guess that this crystal was never tested with any X-ray source. After all George is a physicist who study photosynthesis processes by spectroscopic methods. However (unrelated but connected) I have collected once a data set from a see urchin needle which was 1 cm long, about 3 mm across (protein mass was dissolved), it was a single crystal despite a complicated and beautiful architecture, and mosaicity was about 0.5 deg on a Rigaku AFC5 diffractometer (mounted on a rotating anode with Ni filter. So I would not bet on the large crystal - big mosaicity formula. FF This remarkable hollow 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 Oct 25, 2013, at 16:54 , Derek Logan derek.lo...@biochemistry.lu.se wrote: Hi Felix, What was the mosaicity of this crystal? The absorption correction must have been challenging too... Derek On 25 Oct 2013, at 13:23, Felix Frolow mbfro...@post.tau.ac.il wrote: Well if we start recalling rumours, I have heard that in UC San Diego in the laboratory of George Feher there was (is) a tetragonal hen egg white lysozyme crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. I have never visited George laboratory, but maybe among the society there are some who can shed some light on that…. FF 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 Oct 25, 2013, at 12:18 , Boaz Shaanan bshaa...@bgu.ac.il wrote: Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: 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
Re: [ccp4bb] largest protein crystal ever grown?
Felix, Although I have passed through George's lab at UCSD several times, I have not seen that crystal, but it should be pointed out that George's interests did extend beyond photosynthesis. Some of us older folks remember George's contributions to protein crystal growth, both theoretical and experimental (see Z. Kam, H.B. Shore, and G. Feher, J. Mol. Biol. 123, 539, 1978 or his contribution in Methods in Enzymology, volume 114). So it would not be surprising to find a humungous crystal in his lab; he was interested in the mechanism(s) of crystal growth cessation, which may have led his group to see how big a crystal they could grow. Unfortunately, parts of his lab were often dark when I was visiting due to his photosynthesis experiments. Perhaps Jim Allen or former people from the Kraut and Xuong labs would know. Cheers, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Oct 25, 2013, at 11:13 AM, Felix Frolow wrote: I guess that this crystal was never tested with any X-ray source. After all George is a physicist who study photosynthesis processes by spectroscopic methods. However (unrelated but connected) I have collected once a data set from a see urchin needle which was 1 cm long, about 3 mm across (protein mass was dissolved), it was a single crystal despite a complicated and beautiful architecture, and mosaicity was about 0.5 deg on a Rigaku AFC5 diffractometer (mounted on a rotating anode with Ni filter. So I would not bet on the large crystal - big mosaicity formula. FF This remarkable hollow 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 Oct 25, 2013, at 16:54 , Derek Logan derek.lo...@biochemistry.lu.se wrote: Hi Felix, What was the mosaicity of this crystal? The absorption correction must have been challenging too... Derek On 25 Oct 2013, at 13:23, Felix Frolow mbfro...@post.tau.ac.il wrote: Well if we start recalling rumours, I have heard that in UC San Diego in the laboratory of George Feher there was (is) a tetragonal hen egg white lysozyme crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. I have never visited George laboratory, but maybe among the society there are some who can shed some light on that…. FF 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 Oct 25, 2013, at 12:18 , Boaz Shaanan bshaa...@bgu.ac.il wrote: Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: 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,
[ccp4bb] CCP4-6.4.0 Update 001
Dear CCP4 Users, An update for the new CCP4-6.4.0 series has just been released, consisting of the following changes: • Qt libraries (Mac, Linux): critical fixes for some Mac OSX setups and for KDE desktops • TclTk libraries (Linux): recompiled to be made functional on CentOS4 • TclTk libraries (Windows): fixes that make fresh ccp4 installation work without rebooting • Coot (Mac): fixed keyboard shortcuts • Coot (Linux): now runs from command lines without sourcing ccp4 • MrBUMP (all): fixed MAFFT option • AMPLE (Mac, Linux): added subtask for membrane proteins; bug fixes for Mac • Xia2 (Mac, Linux): update to Xia2 release 0.3.6.3 (fixes ctruncate issue) • QtRView (all): fixes that allow display of large summaries, e.g. from aimless • iMosflm (Linux): fixed critical issue on 32 bit Linuxes Note that auto-updates work only with CCP4 6.4.0 series, therefore upgrade if necessary. Update Manager is now included in the package so you do not need to install it separately. In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation. Please report any bugs to c...@stfc.ac.uk Many thanks for using CCP4 Andrey Lebedev -- Scanned by iCritical.
[ccp4bb] Unusual electron density - any guesses??
Dear All, I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. The model is pretty much finished but I see a strange electron density that I can't imagine what it is. Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ . Any pointers/guesses are most welcome. In short, I see an oblong piece of density coming straight out of the main-chain!! It doesn't refine as a chain of waters and any small piece of PEG doesn't refine properly either (actually, not sure if this would make any sense but since the crystallization condition is PEG3350 and gave it a try!!). The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. The protein was purified from recombinant expression in E. coli with trivial reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... Wishing you all an excellent weekend, best regards, Jose -- * José Artur Brito, PhD* * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal* * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt *
Re: [ccp4bb] Unusual electron density - any guesses??
Is that a glycine in the sequence next to the Glu/Gln? Have you tried building a 50% occ of the backbone in that region in two conformations, and then a water molecule further up into the feature. The density over the carbonyl looks weak and you have some negative density there that might indicate mixed conformation. Just an idea, hard to tell from still images if my idea would work. Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jose Artur Brito Sent: Friday, October 25, 2013 1:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unusual electron density - any guesses?? Dear All, I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. The model is pretty much finished but I see a strange electron density that I can't imagine what it is. Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ . Any pointers/guesses are most welcome. In short, I see an oblong piece of density coming straight out of the main-chain!! It doesn't refine as a chain of waters and any small piece of PEG doesn't refine properly either (actually, not sure if this would make any sense but since the crystallization condition is PEG3350 and gave it a try!!). The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. The protein was purified from recombinant expression in E. coli with trivial reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... Wishing you all an excellent weekend, best regards, Jose -- * José Artur Brito, PhD* * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal* * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt *
[ccp4bb] In need of SGI computer genius
Hello all, OK - small school - old NMR (really old). We set this up around 14 years ago with an O2 system as the user interface, with an indigo system as the interface between the O2 and the NMR. This is a JEOL system, has really been a workhorse with little issues over the last 14 years. We are obviously at the end here. We are working on getting a new one - but that's a work in progress. Anyway - today the hard drive failed on the indigo system. The simple issue is this - we access the indigo strictly via telnet. I do have a backup (I believe) on tape of the indigo. What is the best way to proceed here? There is no monitor on the indigo (nor is there a keyboard). I don't even have a monitor for it (no graphics card - and I don't have an old terminal). Thanks Dave
Re: [ccp4bb] In need of SGI computer genius
Does this help? http://www.nekochan.net/wiki/Headless Not sure, how you'd set it to output to the serial port with the commands if you can't see what you're doing in the first place though. Otherwise you'll have to look for a graphics card that'll work in an indigo, a ps/2 keyboard mouse, and a sync on green monitor. On Fri, Oct 25, 2013 at 1:14 PM, David Roberts drobe...@depauw.edu wrote: Hello all, OK - small school - old NMR (really old). We set this up around 14 years ago with an O2 system as the user interface, with an indigo system as the interface between the O2 and the NMR. This is a JEOL system, has really been a workhorse with little issues over the last 14 years. We are obviously at the end here. We are working on getting a new one - but that's a work in progress. Anyway - today the hard drive failed on the indigo system. The simple issue is this - we access the indigo strictly via telnet. I do have a backup (I believe) on tape of the indigo. What is the best way to proceed here? There is no monitor on the indigo (nor is there a keyboard). I don't even have a monitor for it (no graphics card - and I don't have an old terminal). Thanks Dave
Re: [ccp4bb] In need of SGI computer genius
On Oct 25, 2013, at 11:14 , David Roberts drobe...@depauw.edu wrote: Hello all, OK - small school - old NMR (really old). We set this up around 14 years ago with an O2 system as the user interface, with an indigo system as the interface between the O2 and the NMR. This is a JEOL system, has really been a workhorse with little issues over the last 14 years. We are obviously at the end here. We are working on getting a new one - but that's a work in progress. Anyway - today the hard drive failed on the indigo system. The simple issue is this - we access the indigo strictly via telnet. I do have a backup (I believe) on tape of the indigo. What is the best way to proceed here? There is no monitor on the indigo (nor is there a keyboard). I don't even have a monitor for it (no graphics card - and I don't have an old terminal). I'd suggest first restoring the tape backup onto another machine on the network. Then, you could access the console on the Indigo via a serial cable [from Sabuj's post--many more recent machines appear to lack a serial port, but you can get RS232 = USB adaptors for cheap that work well enough], and configure the Indigo to netboot off the restored tape backup. // Johan Postdoctoral Fellow @ Physical Biosciences Division ___ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
Re: [ccp4bb] largest protein crystal ever grown?
crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. Sounds like a crystallographic legend, beautiful but never achievable… Happy Halloween! Alexander Aleshin Sanford-Burnham Medical Research Institute La Jolla, California On Oct 25, 2013, at 4:23 AM, Felix Frolow wrote: Well if we start recalling rumours, I have heard that in UC San Diego in the laboratory of George Feher there was (is) a tetragonal hen egg white lysozyme crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. I have never visited George laboratory, but maybe among the society there are some who can shed some light on that…. FF 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.ilmailto:mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 25, 2013, at 12:18 , Boaz Shaanan bshaa...@bgu.ac.ilmailto:bshaa...@bgu.ac.il wrote: Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK נושא: 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.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/ -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.sehttp://www.cmps.lu.se/ Centre for Molecular Protein Science www.maxlab.lu.se/node/307http://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.demailto: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
[ccp4bb] strange unit cell
Hi, I tried to find out a correct space group using the program Zanuda. Surprisingly, Zanuda suggested a space group P42212 but not P21 and cubic ones. The unit cell of P42212 was 104.240 104.240 104.209 90.00 90.00 90.00. The number of molecules in an AU was 1, while there were 4 molecules in an AU of P21, and after refinement, R values were 0.199/0.247. I think it seems like a correct space group. So, I’m going to carry out re- processing. Thank you for all your help. Best regards, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
