Re: [ccp4bb] birefringent spacegroups
Hi Jacob, The birefringence of a crystal is determined by a three dimensional shape (the indicatrix) describing how refractive index varies with direction within the crystal. You can think of this as a 3d ellipse and the birefringence is given by the difference in length of the two axes of the ellipse 'seen' by light as it passes through the crystal. The orientation and shape of the indicatrix are constrained by the point group symmetry of the crystal. In the case of cubic crystals, the indicatrix is characterised by four 3-fold axes. The indicatrix for all cubic crystals is thus a sphere and cubic crystals are non-birefringent. Hexagonal, trigonal and tetragonal crystals are uniaxial and the indicatrix is an ellipsoid of revolution - there is one direction in which the crystal appears non-birefringent. Orthorhombic, monoclinic and triclinic systems are biaxial -two axes in which the crystal appears non-birefringent. A good reference is Nye (1984). Physical Properties of crystals. Their representation by tensors and matrices. Clarendon Press, Oxford. There is a more detailed list of space groups and their tensor optical properties in there I think. Cheers, Robin Jacob Keller wrote: Dear Crystallographers, is there a list somewhere of spacegroups which can and cannot be birefringent? Upon what feature of the spacegroup does this depend? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
Re: [ccp4bb] birefringent spacegroups
Hi Jacob, Chek out Section 2 in the following paper: Echalier et al. (2004) Assessing crystallization droplets uding birefringence. Acta Cryst D60, 696-702. It offers a very effective summary of the physical basis of crystal birefringence and reiterates the classification of crystal optics based on isotropic, uniaxial and biaxial systems. My understanding is that a favorable crystal orientation with respect to the direction of view is important for being able to observe appreciable birefringence from uniaxial and biaxial crystals. This can be especially tricky to get from biaxial crystals, i.e. crystals with orthorhombic or monoclinic or triclinic point-group symmetry, projecting their optically anisotropic axis in the plane of the view. Crystals with cubic symmetry are optically isotropic and are therefore not birefringent. Best wishes Savvas -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller Sent: Thursday, June 12, 2008 2:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] birefringent spacegroups Dear Crystallographers, is there a list somewhere of spacegroups which can and cannot be birefringent? Upon what feature of the spacegroup does this depend? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
[ccp4bb] need test data set
Dear scientists and friends, I am much interested to learn things by my own. There are many guys out there as me. To fulfill the thirst and quest for more crystallographic practical knowledge, I need test data set for SAD,MAD,SIR,MIR,SIRAS,MIRAS. And I want to remind kevin and Martyn that they told they will give link for the test dataset to play with most of the ccp4 programs in the wiki. (during recent bioxhit ,oulu workshop) where can i get them, is there any scientist ready to provide. -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
Re: [ccp4bb] need test data set
Hi, For MR/SAD/MAD data, the JCSG have made most of their data available - the processed data at a number of stages (integrated, scaled etc.) and quite a lot of the raw diffraction data. If you google jcsg they are the first hit. If you look at the structure gallery you can download all the files, though you do need to register. I know a great many methods developers use this resource for testing software out, so it is certainly a good place to start. Cheers, Graeme From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jayashankar Sent: 12 June 2008 13:41 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] need test data set Dear scientists and friends, I am much interested to learn things by my own. There are many guys out there as me. To fulfill the thirst and quest for more crystallographic practical knowledge, I need test data set for SAD,MAD,SIR,MIR,SIRAS,MIRAS. And I want to remind kevin and Martyn that they told they will give link for the test dataset to play with most of the ccp4 programs in the wiki. (during recent bioxhit ,oulu workshop) where can i get them, is there any scientist ready to provide. -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
Re: [ccp4bb] need test data set
Hi We have just launched TARDIS - a federated repository for raw diffraction data: http://www.tardis.edu.au/ So far it contains MR/MIRAS data, but will expand soon cheers Ashley On 12/06/2008, at 10:40 PM, Jayashankar wrote: Dear scientists and friends, I am much interested to learn things by my own. There are many guys out there as me. To fulfill the thirst and quest for more crystallographic practical knowledge, I need test data set for SAD,MAD,SIR,MIR,SIRAS,MIRAS. And I want to remind kevin and Martyn that they told they will give link for the test dataset to play with most of the ccp4 programs in the wiki. (during recent bioxhit ,oulu workshop) where can i get them, is there any scientist ready to provide. -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Ashley Buckle Ph.D NHMRC Senior Research Fellow The Department of Biochemistry and Molecular Biology School of Biomedical Sciences, Faculty of Medicine Victorian Bioinformatics Consortium (VBC) Monash University, Clayton, Vic 3800 Australia http://www.med.monash.edu.au/biochem/staff/abuckle.html iChat/AIM: blindcaptaincat skype: ashley.buckle Tel: (613) 9902 0269 (office) Tel: (613) 9905 1653 (lab) Fax : (613) 9905 4699
[ccp4bb] AW: [ccp4bb] topology diagram
Hi Neeraj, Try pdbsum. looks nice for mine. You can upload your structure there... http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/upload.html hth... gregor -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von Neeraj Gesendet: Mittwoch, 11. Juni 2008 17:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] topology diagram Hi all, wondering if anyone knows of a user friendly and esy to use program for generating topology diagrams for proteins. Any help would be very useful to me. thanks, Neeraj -- Neeraj Kapoor TPCB Graduate Fellow Sakmar Lab/ Molecular Biology Biochemistry The Rockefeller University 1230 York Avenue, RRB 510 New York, NY 10021 lab.1.212.327.8284:fax.7904 mobile: 917.535.2030 http://www.rockefeller.edu/labheads/sakmar/sakmar-lab.html
Re: [ccp4bb] need test data set
The crank/dm/buccaneer tutorial is now available here: http://www.ysbl.york.ac.uk/~cowtan/buccaneer/tutorial/tutorial.html More data is available in your $CEXAM directory. There are datasets for RNAse and toxd dataset - both SIR/MIR. In the CVS version there is also SIRAS data for rnase and a Gere dataset - see http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/examples/. Beyond that, the JCSG is probably the place to go. Jayashankar wrote: Dear scientists and friends, I am much interested to learn things by my own. There are many guys out there as me. To fulfill the thirst and quest for more crystallographic practical knowledge, I need test data set for SAD,MAD,SIR,MIR,SIRAS,MIRAS. And I want to remind kevin and Martyn that they told they will give link for the test dataset to play with most of the ccp4 programs in the wiki. (during recent bioxhit ,oulu workshop) where can i get them, is there any scientist ready to provide. -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
Re: [ccp4bb] need test data set
Jayashankar schrieb: Dear scientists and friends, I am much interested to learn things by my own. There are many guys out there as me. To fulfill the thirst and quest for more crystallographic practical knowledge, I need test data set for SAD,MAD,SIR,MIR,SIRAS,MIRAS. And I want to remind kevin and Martyn that they told they will give link for the test dataset to play with most of the ccp4 programs in the wiki. (during recent bioxhit ,oulu workshop) where can i get them, is there any scientist ready to provide. -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany check out the Quality control article in XDSwiki ( http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Quality_Control ) - it has 4 datasets and structure solutions - more to come. HTH, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle
I assume you are talking about a sugar-binding enzyme ;) I have some aspects to consider in addition to what Artem raises. Many effects of a mutation are not recognizable in a static crystal structure or even in an NMR structure. For example, it is usually difficult to assess the thermodynamics of substrate binding, not to mention the kinetics. Multi-valent substrates usually display some sort of cooperativity for the binding process, which you might have affected by mutating one of the subsites. You might be able to obtain some hints from a Michaelis- Menten analysis of the mutant compared to the wild type, but that would only be a start. Your crystallographic result of a less occupied substrate-binding site for the mutant serves as a hint as well, but such results are hardly conclusive. You will have to follow up with more rigorous methods, such as ITC (thermodynamics of binding) and time-resolved methods (kinetics of binding). One example of an effect of a mutation that is usually not recognizable in a crystal structure has to do with substrate guiding. In this case, the mutation has changed the surface of the protein, thus affecting how well the multi-valent substrate can approach and wiggle itself into the binding site. Once in the binding site, it is structurally virtually indistinguishable from the wild-type. Ah, the nightmares of interpreting crystal structures in terms of biology! Good luck! Best - MM On Jun 11, 2008, at 7:21 PM, Narayanan Ramasubbu wrote: Dear all: I have a single residue mutant whose enzyme activity is about 50% of the wild type. Interestingly, the mutation is in a region that involves a secondary site but not the active site. The two structures with or without ligands fit well (0.18 A) and the metal binding and cofactor binding sites are all preserved in the mutant. The one difference noticed is that the ligand does not fill the active site (partially occupied subsites) unlike the wild type where all the subsites are occupied. Water structure around the actives site residues are identical. I looked at the electrostatics and both surfaces look similar (not an expert). There are some residues whose sides chains show some positional disorder and these residues are at the edges of the active site. The resolution of the both data sets are 1.5A. The mutant enzyme was derived by MR. One another possibility that I want to look at is to compare the compactness of the two enzyme structures. What is the best way to compare that? I am wondering whether the breathing that was mentioned for some enzymes might be playing a role in the mutant enzyme. Also, I would appreciate comments on other possible explanations for this unusual (?) behavior. Thanks a lot Subbu Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
Re: [ccp4bb] birefringent spacegroups
On Wednesday 11 June 2008 23:55, Robin Owen wrote: Hi Jacob, The birefringence of a crystal is determined by a three dimensional shape (the indicatrix) describing how refractive index varies with direction within the crystal. You can think of this as a 3d ellipse and the birefringence is given by the difference in length of the two axes of the ellipse 'seen' by light as it passes through the crystal. The orientation and shape of the indicatrix are constrained by the point group symmetry of the crystal. In the case of cubic crystals, the indicatrix is characterised by four 3-fold axes. The indicatrix for all cubic crystals is thus a sphere and cubic crystals are non-birefringent. Hexagonal, trigonal and tetragonal crystals are uniaxial and the indicatrix is an ellipsoid of revolution - there is one direction in which the crystal appears non-birefringent. Orthorhombic, monoclinic and triclinic systems are biaxial -two axes in which the crystal appears non-birefringent. I have wondered about this in the past. That argument only appears to hold if birefringent is taken to mean different optical index at two angles 90 degrees apart. I think even in a cubic crystal you can find non-equivalent directions if you are not limited to a right angle between the two vectors. Does this not count as birefringence? Or am I misunderstanding the definition? Ethan and then there's the issue of anomalous dispersion... A good reference is Nye (1984). Physical Properties of crystals. Their representation by tensors and matrices. Clarendon Press, Oxford. There is a more detailed list of space groups and their tensor optical properties in there I think. Cheers, Robin Jacob Keller wrote: Dear Crystallographers, is there a list somewhere of spacegroups which can and cannot be birefringent? Upon what feature of the spacegroup does this depend? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle
On a general note, it is not unusual at all for a random mutation (i.e., one not in the active or regulatory site of an enzyme, and not significantly connected with the catalytic or regulatory mechanism) to affect the rate constant of an enzyme-catalyzed reaction (kcat or kcat/Km) by a factor of 2 or more. Most enzyme kineticists don't get too excited about assigning an important role to a mutated residue unless one of the rate constants changes by a factor of 10. One danger in interpreting mutagenesis experiments is doing only a single kinetics measurement at a fixed pH and/or substrate concentration. If the mutation affects the pKa of enzyme catalytic groups or the effective Km of the substrate, a difference in rate will be noted, even though the fundamental rate constants kcat or kcat/Km, or their pH-independent maximal values, may not have significantly changed. Just my $0.02. -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Mischa Machius wrote: I assume you are talking about a sugar-binding enzyme ;) I have some aspects to consider in addition to what Artem raises. Many effects of a mutation are not recognizable in a static crystal structure or even in an NMR structure. For example, it is usually difficult to assess the thermodynamics of substrate binding, not to mention the kinetics. Multi-valent substrates usually display some sort of cooperativity for the binding process, which you might have affected by mutating one of the subsites. You might be able to obtain some hints from a Michaelis- Menten analysis of the mutant compared to the wild type, but that would only be a start. Your crystallographic result of a less occupied substrate-binding site for the mutant serves as a hint as well, but such results are hardly conclusive. You will have to follow up with more rigorous methods, such as ITC (thermodynamics of binding) and time-resolved methods (kinetics of binding). One example of an effect of a mutation that is usually not recognizable in a crystal structure has to do with substrate guiding. In this case, the mutation has changed the surface of the protein, thus affecting how well the multi-valent substrate can approach and wiggle itself into the binding site. Once in the binding site, it is structurally virtually indistinguishable from the wild-type. Ah, the nightmares of interpreting crystal structures in terms of biology! Good luck! Best - MM On Jun 11, 2008, at 7:21 PM, Narayanan Ramasubbu wrote: Dear all: I have a single residue mutant whose enzyme activity is about 50% of the wild type. Interestingly, the mutation is in a region that involves a secondary site but not the active site. The two structures with or without ligands fit well (0.18 A) and the metal binding and cofactor binding sites are all preserved in the mutant. The one difference noticed is that the ligand does not fill the active site (partially occupied subsites) unlike the wild type where all the subsites are occupied. Water structure around the actives site residues are identical. I looked at the electrostatics and both surfaces look similar (not an expert). There are some residues whose sides chains show some positional disorder and these residues are at the edges of the active site. The resolution of the both data sets are 1.5A. The mutant enzyme was derived by MR. One another possibility that I want to look at is to compare the compactness of the two enzyme structures. What is the best way to compare that? I am wondering whether the breathing that was mentioned for some enzymes might be playing a role in the mutant enzyme. Also, I would appreciate comments on other possible explanations for this unusual (?) behavior. Thanks a lot Subbu Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle
Hi Subbu, Here's my two cents. Your project sounds really interesting. You mentioned in your email that the active site and associated waters in the active site of the wild type and mutant enzymes are identical. It's worth noting that even very small (on the 1/10th of an angstrom level) structural perturbations can have impacts on protein function. When high pressure is applied to some enzymes, their activities can be affected by factors of 2 or 4, or perhaps even more. The structural deformations due to high pressures (1000 x atmospheric) are often on the sub-angstrom level. If you have sufficient crystals, I might be tempted to re-solve the mutant and wild type structure a few times with fresh data, and get a feel for how much error exists is in the position of key residues. This might tell you how close the geometry of the two active sites really are. Good luck! and all the best, --Buz On Jun 11, 2008, at 8:21 PM, Narayanan Ramasubbu wrote: Dear all: I have a single residue mutant whose enzyme activity is about 50% of the wild type. Interestingly, the mutation is in a region that involves a secondary site but not the active site. The two structures with or without ligands fit well (0.18 A) and the metal binding and cofactor binding sites are all preserved in the mutant. The one difference noticed is that the ligand does not fill the active site (partially occupied subsites) unlike the wild type where all the subsites are occupied. Water structure around the actives site residues are identical. I looked at the electrostatics and both surfaces look similar (not an expert). There are some residues whose sides chains show some positional disorder and these residues are at the edges of the active site. The resolution of the both data sets are 1.5A. The mutant enzyme was derived by MR. One another possibility that I want to look at is to compare the compactness of the two enzyme structures. What is the best way to compare that? I am wondering whether the breathing that was mentioned for some enzymes might be playing a role in the mutant enzyme. Also, I would appreciate comments on other possible explanations for this unusual (?) behavior. Thanks a lot Subbu
Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle
Let us not forget about the very fact that X-ray is an ionizing radiation and a potent creator of radicals! Please see these references - seeing a crystal that was purple in the middle (0.3mm radius of beam) and perfectly yellow at edges (crystal was 0.5mm long) was an eye opening experience. How many of you keep looking at the crystal during data collection in color? And pay attention to it at all? Not every reaction makes such dramatic effect either - it could as well be 'silent'. Even in this case...I had to put a real fight to publish because one reviewer accused me of some voo-doo (not in such words, but...) saying that I cannot find in the structure what I did not put in. He he he he I wonder how many examples of that are out and documented? :) Ewa Int. J. Molecular Medicine 12(1), 17-24, 2003 and 6, 521-6, 2000. Dr Ewa Skrzypczak-Jankun Associate Professor University of Toledo Office: Dowling Hall r.2257 Health Science Campus Phone: 419-383-5414 Urology Department Mail Stop #1091 Fax: 419-383-3785 3000 Arlington Ave. e-mail: [EMAIL PROTECTED] Toledo OH 43614-2598 web: http://golemxiv.dh.meduohio.edu/~ewa -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mischa Machius Sent: Thursday, June 12, 2008 10:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle I assume you are talking about a sugar-binding enzyme ;) I have some aspects to consider in addition to what Artem raises. Many effects of a mutation are not recognizable in a static crystal structure or even in an NMR structure. For example, it is usually difficult to assess the thermodynamics of substrate binding, not to mention the kinetics. Multi-valent substrates usually display some sort of cooperativity for the binding process, which you might have affected by mutating one of the subsites. You might be able to obtain some hints from a Michaelis- Menten analysis of the mutant compared to the wild type, but that would only be a start. Your crystallographic result of a less occupied substrate-binding site for the mutant serves as a hint as well, but such results are hardly conclusive. You will have to follow up with more rigorous methods, such as ITC (thermodynamics of binding) and time-resolved methods (kinetics of binding). One example of an effect of a mutation that is usually not recognizable in a crystal structure has to do with substrate guiding. In this case, the mutation has changed the surface of the protein, thus affecting how well the multi-valent substrate can approach and wiggle itself into the binding site. Once in the binding site, it is structurally virtually indistinguishable from the wild-type. Ah, the nightmares of interpreting crystal structures in terms of biology! Good luck! Best - MM On Jun 11, 2008, at 7:21 PM, Narayanan Ramasubbu wrote: Dear all: I have a single residue mutant whose enzyme activity is about 50% of the wild type. Interestingly, the mutation is in a region that involves a secondary site but not the active site. The two structures with or without ligands fit well (0.18 A) and the metal binding and cofactor binding sites are all preserved in the mutant. The one difference noticed is that the ligand does not fill the active site (partially occupied subsites) unlike the wild type where all the subsites are occupied. Water structure around the actives site residues are identical. I looked at the electrostatics and both surfaces look similar (not an expert). There are some residues whose sides chains show some positional disorder and these residues are at the edges of the active site. The resolution of the both data sets are 1.5A. The mutant enzyme was derived by MR. One another possibility that I want to look at is to compare the compactness of the two enzyme structures. What is the best way to compare that? I am wondering whether the breathing that was mentioned for some enzymes might be playing a role in the mutant enzyme. Also, I would appreciate comments on other possible explanations for this unusual (?) behavior. Thanks a lot Subbu Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
[ccp4bb] Post-doc and technician position in NKI, Amsterdam
A post-doctoral position and a technician position available in the Netherlands Cancer Institute in the groups of Titia Sixma. The Netherlands Cancer Institute is a center of excellence with a high standard of biological research and an interactive atmosphere. It is located in Amsterdam, with all its cultural amenities, close to Schiphol airport. The group has an interest in structural studies coupled to functional analysis. We share meetings and lab-space with the group of Tassos Perrakis, who amongst other things has an interest in method development for structural biology. Equipment includes expression in mammalian and insect cells, high throughput crystallization, in-house X-ray facility (MarDTB with Bruker optics), surface plasmon resonance (Biacore), isothermal titration calorimetry, static light scattering (MALLS), mass spectrometry etc. The project focuses on the ligand binding process in cys-loop receptors. We study these pentameric ion-channels, for which the nicotinic acetylcholine receptor is the prototype, primarily through structure-function analysis on the model protein AChBP. Using a combination of biophysical analysis and protein crystallography and we collaborate closely with neurobiologists (Guus Smit, VU, Amsterdam), chemists interested in drug design (e.g. de Esch, VU) and electrophysiologists (Bertrand, Geneva) as well as other members of the EU-network Neurocypres. We are looking for enthusiastic researchers with experience in protein crystallography, molecular biology and/or biochemistry. Applicants should write an e-mail with CV and names of three references to [EMAIL PROTECTED] Titia Sixma Prof. Titia K. Sixma, Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam,The Netherlands Phone: +31-20-5121959/50, Fax: +31-20-5121954, E-mail: [EMAIL PROTECTED] , Website: http://xtal.nki.nl
Re: [ccp4bb] birefringent spacegroups
Hi Ethan You could be right, see this paper: http://physics.nist.gov/Divisions/Div842/Gp2/DUVMatChar/PDF/IntBiref.pdf Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt Sent: 12 June 2008 15:46 To: Multiple recipients Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] birefringent spacegroups On Wednesday 11 June 2008 23:55, Robin Owen wrote: Hi Jacob, The birefringence of a crystal is determined by a three dimensional shape (the indicatrix) describing how refractive index varies with direction within the crystal. You can think of this as a 3d ellipse and the birefringence is given by the difference in length of the two axes of the ellipse 'seen' by light as it passes through the crystal. The orientation and shape of the indicatrix are constrained by the point group symmetry of the crystal. In the case of cubic crystals, the indicatrix is characterised by four 3-fold axes. The indicatrix for all cubic crystals is thus a sphere and cubic crystals are non-birefringent. Hexagonal, trigonal and tetragonal crystals are uniaxial and the indicatrix is an ellipsoid of revolution - there is one direction in which the crystal appears non-birefringent. Orthorhombic, monoclinic and triclinic systems are biaxial -two axes in which the crystal appears non-birefringent. I have wondered about this in the past. That argument only appears to hold if birefringent is taken to mean different optical index at two angles 90 degrees apart. I think even in a cubic crystal you can find non-equivalent directions if you are not limited to a right angle between the two vectors. Does this not count as birefringence? Or am I misunderstanding the definition? Ethan and then there's the issue of anomalous dispersion... A good reference is Nye (1984). Physical Properties of crystals. Their representation by tensors and matrices. Clarendon Press, Oxford. There is a more detailed list of space groups and their tensor optical properties in there I think. Cheers, Robin Jacob Keller wrote: Dear Crystallographers, is there a list somewhere of spacegroups which can and cannot be birefringent? Upon what feature of the spacegroup does this depend? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] JCSG dataset archive
All, Thanks to everyone who has recently requested access to the JCSG dataset archive. We have a large and growing number of users. Your requests will be handled shortly and you will receive notification via e-mail. Our registered users fall into 3 main classes: 1) Methods developers who want access to a wide array of test data. 2) Students and postdocs who want datasets for training purposes. 3) Researchers interested in one of our structures, who want access To all the data we have available, including datasets from different constructs or crystal forms that didn't necessarily make it into our final PDB deposition. For those who may still be interested, the dataset archive can be accessed through our structure gallery page: http://www.jcsg.org/prod/scripts/structure_gallery/gallery.shtml The datasets are available without restriction, most of them are Se MAD/SAD or distant homology MR. We do ask you to register and explain why you want access. This is largely for tracking/statistics purposes (we won't be sending you a lot of junk mail). Hopefully in the future we can improve the system to better serve our users. Soon we will be adding diffraction image datasets for *all* our structures as Soon as they are deposited. In the meantime, if there is a dataset you would like that is not currently available through the archive just drop me an e-mail. Suggestions are always welcome. Sincerely, Ashley Deacon Joint Center for Structural Genomics.
Re: [ccp4bb] birefringent spacegroups
PS in case you missed it, here's the bottom line from the paper: Interestingly, a cubic crystal has seven nonbirefringent axes, four in the 111 directions and three in the 100 directions, with birefringence maxima in the twelve 110 directions. So it would appear that the optical properties of cubic crystals are *more* complicated than those of lower symmetry systems, not less! - and previous conclusions about isotropy of cubic crystals probably arose because the measurements were simply not precise enough (or not carried out at short enough wavelength) to detect the effect. However the relevant theory goes back to Lorentz (1878) so it's not exactly new! Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: 12 June 2008 17:50 To: Ethan A Merritt; Jacob Keller Cc: CCP4BB@jiscmail.ac.uk Subject: RE: [ccp4bb] birefringent spacegroups Hi Ethan You could be right, see this paper: http://physics.nist.gov/Divisions/Div842/Gp2/DUVMatChar/PDF/IntBiref.pdf Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt Sent: 12 June 2008 15:46 To: Multiple recipients Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] birefringent spacegroups On Wednesday 11 June 2008 23:55, Robin Owen wrote: Hi Jacob, The birefringence of a crystal is determined by a three dimensional shape (the indicatrix) describing how refractive index varies with direction within the crystal. You can think of this as a 3d ellipse and the birefringence is given by the difference in length of the two axes of the ellipse 'seen' by light as it passes through the crystal. The orientation and shape of the indicatrix are constrained by the point group symmetry of the crystal. In the case of cubic crystals, the indicatrix is characterised by four 3-fold axes. The indicatrix for all cubic crystals is thus a sphere and cubic crystals are non-birefringent. Hexagonal, trigonal and tetragonal crystals are uniaxial and the indicatrix is an ellipsoid of revolution - there is one direction in which the crystal appears non-birefringent. Orthorhombic, monoclinic and triclinic systems are biaxial -two axes in which the crystal appears non-birefringent. I have wondered about this in the past. That argument only appears to hold if birefringent is taken to mean different optical index at two angles 90 degrees apart. I think even in a cubic crystal you can find non-equivalent directions if you are not limited to a right angle between the two vectors. Does this not count as birefringence? Or am I misunderstanding the definition? Ethan and then there's the issue of anomalous dispersion... A good reference is Nye (1984). Physical Properties of crystals. Their representation by tensors and matrices. Clarendon Press, Oxford. There is a more detailed list of space groups and their tensor optical properties in there I think. Cheers, Robin Jacob Keller wrote: Dear Crystallographers, is there a list somewhere of spacegroups which can and cannot be birefringent? Upon what feature of the spacegroup does this depend? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused
Re: [ccp4bb] birefringent spacegroups
On Thursday 12 June 2008 11:19, Philippe DUMAS wrote: Hello, A short comment of historical interest: the first theory about double refraction in crystals (with explicit calculation of the index ellipsoid) goes back to 3 memoirs by A. Fresnel in 1821 and 1822. So, we are even in older regions. This being said, in cubic crystals the index ellipsoid can only be a sphere. But the ellipsoid is only a convenient approximation based on properties evaluated at 3 orthogonal axes. It is not a complete description, it is simple model. More complex models may describe more complex properties, as is the case in the paper that Ian refers to. And so, no birefringence should exist If birefringence is formally defined in terms of the approximating ellipsoid, this is correct. I do not know if this is the case or not. But if birefringence is generalized to mean optical index varies with incident illumination vector then I believe all protein crystals are birefringent. I may be talking nonsense here. If so, I welcome the opportunity to learn better. Ethan (unless there is some external cause of anisotropy: mecanical stress, electric field,...). See Born Wolff (principles of optics) p. 703. May be, our biological crystals might quite easily develop such stress birefringence... Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ian Tickle Envoyé : Thursday, June 12, 2008 7:19 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] birefringent spacegroups PS in case you missed it, here's the bottom line from the paper: Interestingly, a cubic crystal has seven nonbirefringent axes, four in the 111 directions and three in the 100 directions, with birefringence maxima in the twelve 110 directions. So it would appear that the optical properties of cubic crystals are *more* complicated than those of lower symmetry systems, not less! - and previous conclusions about isotropy of cubic crystals probably arose because the measurements were simply not precise enough (or not carried out at short enough wavelength) to detect the effect. However the relevant theory goes back to Lorentz (1878) so it's not exactly new! Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: 12 June 2008 17:50 To: Ethan A Merritt; Jacob Keller Cc: CCP4BB@jiscmail.ac.uk Subject: RE: [ccp4bb] birefringent spacegroups Hi Ethan You could be right, see this paper: http://physics.nist.gov/Divisions/Div842/Gp2/DUVMatChar/PDF/IntBiref.pdf Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt Sent: 12 June 2008 15:46 To: Multiple recipients Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] birefringent spacegroups On Wednesday 11 June 2008 23:55, Robin Owen wrote: Hi Jacob, The birefringence of a crystal is determined by a three dimensional shape (the indicatrix) describing how refractive index varies with direction within the crystal. You can think of this as a 3d ellipse and the birefringence is given by the difference in length of the two axes of the ellipse 'seen' by light as it passes through the crystal. The orientation and shape of the indicatrix are constrained by the point group symmetry of the crystal. In the case of cubic crystals, the indicatrix is characterised by four 3-fold axes. The indicatrix for all cubic crystals is thus a sphere and cubic crystals are non-birefringent. Hexagonal, trigonal and tetragonal crystals are uniaxial and the indicatrix is an ellipsoid of revolution - there is one direction in which the crystal appears non-birefringent. Orthorhombic, monoclinic and triclinic systems are biaxial -two axes in which the crystal appears non-birefringent. I have wondered about this in the past. That argument only appears to hold if birefringent is taken to mean different optical index at two angles 90 degrees apart. I think even in a cubic crystal you can find non-equivalent directions if you are not limited to a right angle between the two vectors. Does this not count as birefringence? Or am I misunderstanding the definition? Ethan and then there's the issue of anomalous dispersion... A good reference is Nye (1984). Physical Properties of crystals. Their representation by tensors and matrices. Clarendon Press, Oxford. There is a more detailed list of space groups and their tensor optical properties in there I think. Cheers, Robin Jacob Keller wrote: Dear Crystallographers, is there a list somewhere of
[ccp4bb] Density is not clear
Hi all !! I am working with two data sets of same protein (130a/a) with resolutions 2.8 and 3.2 A. In both the cases the density for 100-130 aa is not very clear.. it forms couple of helices.. i can see a long tube going but it is feature less.. It is a MR solution.. i have tried TLS refinement with different TLS groups.. but no luck... i have also tried DM but not much improvement... Data looks clean without any twinning... R and Rfee are around 22.8 and 28.5 for both the structures... Any suggestions?? regards John
Re: [ccp4bb] JCSG dataset archive
I would like to also add that depending on what you want to use the test data for, you may find that the data JCSG has deposited with the PDB is sufficient. The JCSG crystal structures include the following data sections in the structure factor file deposited with the PDB (since spring 2004). 1. First section -- loop over merged Fobs, (or Iobs), sigF (or sigI), Fcalc, Phicalc, FreeR-flag (status) 2. For each wavelength of data used in phasing there is a separate loop over the scaled, unmerged, original index intensities and sigI. 3. Then there is a data loop for the experimental phasing results listing the HL-coefficients from the phasing program (usually autoSHARP or solve). 4. The last loop is over fom, pdbx_fom_weighted_fmap and phase from density modification. The Fmap coefficient and the DM phase is the starting map used for automated model building. (For MR structures, the just the first 2 data sections are present). If you are interested in testing MAD or SAD phasing, DM or autobuilding, algorithms etc, then the data deposited with the PDB is probably sufficient for your needs. http://www.pdb.org/pdb/search/navbarsearch.do?newSearch=yesisAuthorSearch=noradioset=AllinputQuickSearch=JCSG%20crystal If you wanted to reintegrate the data from the diffraction images or if you wanted to compare your autotraced model with the autotraced model we obtained, then these additional data (as well as log files) are only available through the JCSG dataset archive. So as Ashley mentioned, please request access to the archive if you are still interested in this additional data. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Deacon, Ashley Sent: Thursday, June 12, 2008 9:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] JCSG dataset archive All, Thanks to everyone who has recently requested access to the JCSG dataset archive. We have a large and growing number of users. Your requests will be handled shortly and you will receive notification via e-mail. Our registered users fall into 3 main classes: 1) Methods developers who want access to a wide array of test data. 2) Students and postdocs who want datasets for training purposes. 3) Researchers interested in one of our structures, who want access To all the data we have available, including datasets from different constructs or crystal forms that didn't necessarily make it into our final PDB deposition. For those who may still be interested, the dataset archive can be accessed through our structure gallery page: http://www.jcsg.org/prod/scripts/structure_gallery/gallery.shtml The datasets are available without restriction, most of them are Se MAD/SAD or distant homology MR. We do ask you to register and explain why you want access. This is largely for tracking/statistics purposes (we won't be sending you a lot of junk mail). Hopefully in the future we can improve the system to better serve our users. Soon we will be adding diffraction image datasets for *all* our structures as Soon as they are deposited. In the meantime, if there is a dataset you would like that is not currently available through the archive just drop me an e-mail. Suggestions are always welcome. Sincerely, Ashley Deacon Joint Center for Structural Genomics.
Re: [ccp4bb] birefringent spacegroups
But it seems that Hendrik Lorentz was the first to realise that symmetry breaking of the isotropy of the refractive index other optical properties could occur in cubic crystals at sufficiently short wavelength even in the absence of a distorting force - the spatial-dispersion-induced birefringence effect referred to in the paper. Note that this is an intrinsic effect, it has nothing to do with external stress, electric field etc., and if you read the paper you'll see that such external effects were specifically eliminated as the cause of the observed effect. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Philippe DUMAS Sent: 12 June 2008 19:20 To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] birefringent spacegroups Hello, A short comment of historical interest: the first theory about double refraction in crystals (with explicit calculation of the index ellipsoid) goes back to 3 memoirs by A. Fresnel in 1821 and 1822. So, we are even in older regions. This being said, in cubic crystals the index ellipsoid can only be a sphere. An so, no birefringence should exist (unless there is some external cause of anisotropy: mecanical stress, electric field,...). See Born Wolff (principles of optics) p. 703. May be, our biological crystals might quite easily develop such stress birefringence... Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ian Tickle Envoyé : Thursday, June 12, 2008 7:19 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] birefringent spacegroups PS in case you missed it, here's the bottom line from the paper: Interestingly, a cubic crystal has seven nonbirefringent axes, four in the 111 directions and three in the 100 directions, with birefringence maxima in the twelve 110 directions. So it would appear that the optical properties of cubic crystals are *more* complicated than those of lower symmetry systems, not less! - and previous conclusions about isotropy of cubic crystals probably arose because the measurements were simply not precise enough (or not carried out at short enough wavelength) to detect the effect. However the relevant theory goes back to Lorentz (1878) so it's not exactly new! Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: 12 June 2008 17:50 To: Ethan A Merritt; Jacob Keller Cc: CCP4BB@jiscmail.ac.uk Subject: RE: [ccp4bb] birefringent spacegroups Hi Ethan You could be right, see this paper: http://physics.nist.gov/Divisions/Div842/Gp2/DUVMatChar/PDF/In tBiref.pdf Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt Sent: 12 June 2008 15:46 To: Multiple recipients Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] birefringent spacegroups On Wednesday 11 June 2008 23:55, Robin Owen wrote: Hi Jacob, The birefringence of a crystal is determined by a three dimensional shape (the indicatrix) describing how refractive index varies with direction within the crystal. You can think of this as a 3d ellipse and the birefringence is given by the difference in length of the two axes of the ellipse 'seen' by light as it passes through the crystal. The orientation and shape of the indicatrix are constrained by the point group symmetry of the crystal. In the case of cubic crystals, the indicatrix is characterised by four 3-fold axes. The indicatrix for all cubic crystals is thus a sphere and cubic crystals are non-birefringent. Hexagonal, trigonal and tetragonal crystals are uniaxial and the indicatrix is an ellipsoid of revolution - there is one direction in which the crystal appears non-birefringent. Orthorhombic, monoclinic and triclinic systems are biaxial -two axes in which the crystal appears non-birefringent. I have wondered about this in the past. That argument only appears to hold if birefringent is taken to mean different optical index at two angles 90 degrees apart. I think even in a cubic crystal you can find non-equivalent directions if you are not limited to a right angle between the two vectors. Does this not count as birefringence? Or am I misunderstanding the definition? Ethan and then there's the issue of anomalous dispersion... A good reference is Nye (1984). Physical Properties of crystals. Their representation by tensors and matrices. Clarendon Press, Oxford. There is a more detailed list of space groups and their tensor optical properties in there I think. Cheers,
Re: [ccp4bb] Protein binding to Zn and Ca
Thermolysin binds a catalytic zinc and several Ca ions for structural stability. See Holland et al. (1995) Protein Sci, 4, 1955. Hope that helps, Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA On Jun 12, 2008, at 8:15 PM, Neeraj Kapoor wrote: Hi all, I recently came across a question about an interesting idea. Does anyone know of an example of a protein binding to both Zn2+ and Ca2+ at the same time? Are there any known well studied precedents at all if any. Any help of insights would be very valuable. thanks, Neeraj
[ccp4bb] Off topic: insect cell expression
Hi there, nbsp; Sorry for the off topic questions. We need your feedback. nbsp; We are expressing a rat protein in insect cells. It is expressed as a secreted protein with an N-terminal 6xHis tag. We can get about 4 mg of it from 1L culture and everything looked quite normal at the very beginning (at 4C). When I changed the buffer to HBS using centricon to get rid of imidazole (@ 4C), I noticed that it took a long time to concentrate and I saw some ppt. However, when I took some of it (at about 1.2 mg/ml) and kept them at room temperature, the solution turned cloudy in a few minutes. I tried to change the pH by diluted in 1M stock of different buffers (pH 4.5-8.5), change the NaCl concentration, and add 10% glycerol, but it still crashed out at RT. However, it seems OK, I hope,nbsp;when kept on ice. I am wondering whether any of you had a similar experience before. It is not a problem for us to do everything at 4 degree. I just worry that it may indicate something wrong with this protein. The protein should be stable since it has been shaking at 27C for four days… nbsp; Many thanks. nbsp; Best, Chen
