[ccp4bb] dry shippers
Dear all, is anyone using the MVE Bio-Medical IATA/CryoShipper for sending crystals by courier? If you do so, would you please tell me whether it is any good -- especially compared to those others that are more common (e.g. SC 4/2V, CX 100 or similar). Thank you very much, Dirk. --- Dr. DIRK REINERT Protein Crystallography / Structural Research Boehringer Ingelheim Pharma GmbH Co. KG Deutschland Birkendorfer Strasse 65 D-88397 Biberach Phone: +49 (7351) 54-97892 E-mail: [EMAIL PROTECTED] ---
[ccp4bb] NEW POSTDOCTORAL POSITION IN PROTEIN COMPLEX CRYSTALLOGRAPHY (Barcelona)
POSTDOCTORAL POSITION IN PROTEIN COMPLEX CRYSTALLOGRAPHY Applications are invited for a postdoctoral position in Prof. Miquel Colls group at the Institute for Research in Biomedicine / Institut de Biologia Molecular de Barcelona (CSIC) to work on the structural characterization of protein complexes. The position is supported by the EU Project 3D-Repertoire (www.3drepertoire.org http://www.3drepertoire.org/ ). A strong background in protein expression is required. The IRB Barcelona/IBMB laboratories are equipped with state-of-the-art protein expression and purification apparatus, including high-throughput facilities. The crystallographic equipment includes nano-drop crystallization robots, storage and visualization robots, rotating anode generators with image plate detectors, automated sample exchanger and free mounting system, and cutting-edge computational facilities. The Institute is located in the stimulating scientific and cultural environment of the Barcelona Science Park. Those interested should contact (preferably by email): Martha Elisabeth Brigg Secretary Structural and Computational Biology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona, Josep Samitier 1-5 08028 Barcelona, Spain Email [EMAIL PROTECTED] URL: http://www.irbbarcelona.org/mcoll www.irbbarcelona.org/mcoll Applicants should send a full curriculum vitae and the names and addresses (including e-mail address) of two referees no later than Dec 20th, 2007. 29-Nov-2007 Martha Elisabeth Brigg Secretaria de Programa Biologia Estructural i Computacional Institut de Recerca Biomèdica de Barcelona C/ Josep Samitier 1-5 08028 Barcelona, Espanya Tel. +34 93 403 99 53 Fax. +34 93 403 99 76 [EMAIL PROTECTED] www.irbbarcelona.org
[ccp4bb] Postdoc position in Basel
Post-doctoral research position in the Core Program Structural Biology and Biophysics Our group is interested in the molecular mechanisms of solute translocation across bacterial membranes as well as of c-di-GMP signaling. Based on the molecular structures that we determine by X-ray crystallography, hypotheses are tested by analysis of structure - function relationships. Highly motivated, structure oriented candidates with experience in molecular biology, protein chemistry and, preferably, also in biophysical methods and protein crystallography should send a statement of research objectives, a CV and the names of two references to: Tilman Schirmer Structural Biology, Biozentrum University of Basel Klingelbergstrasse 50-70 CH-4056, Basel, Switzerland [EMAIL PROTECTED] http://www.biozentrum.unibas.ch/schirmer
[ccp4bb] Protein interface prediction tool?
Hi, I would like to find a bioinformatic tool that will allow me to predict the dimerisation interface of a protein. A structural model has been generated, and it is known to exist as a homo-dimer. Does anyone know of a suitable program? Thank you for your help. Karen This message was sent using IMP, the Internet Messaging Program.
Re: [ccp4bb] Protein interface prediction tool?
Hey Karen, Pisa analyzes oligomerization interfaces. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Andreas karen yates wrote: Hi, I would like to find a bioinformatic tool that will allow me to predict the dimerisation interface of a protein. A structural model has been generated, and it is known to exist as a homo-dimer. Does anyone know of a suitable program? Thank you for your help. Karen This message was sent using IMP, the Internet Messaging Program.
[ccp4bb] more on dimerization interface analysis
Dear all, Karen question reminded me that I have one also. I study a protein that homodimerizes via a long helix. A number of homologs exist. They all dimerize, but the structure is only known of the first. Homology is high enough that I can easily thread the homologs' sequences onto the structure. How do I go about analyzing the new dimerization interfaces? Before having Pisa have a go, I'd like to do some sort of minimization to allow for wiggling of one helix with respect to the other and rotamerization of side chains. What I'm ultimately interested in is which homologs are likely to form heterooligomers. There is some experimental evidence for that. I'm grateful for suggestions. Andreas -- Andreas Förster Imperial College London https://wasatch.biochem.utah.edu/~andreas
Re: [ccp4bb] Protein interface prediction tool?
HADDOCK..? protein-protein docking.. Dominguez et al., 2003, JACS, 125, 1731-1737 Kristof On 29 Nov 2007, at 13:22, karen yates wrote: Hi, I would like to find a bioinformatic tool that will allow me to predict the dimerisation interface of a protein. A structural model has been generated, and it is known to exist as a homo-dimer. Does anyone know of a suitable program? Thank you for your help. Karen This message was sent using IMP, the Internet Messaging Program. -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] more on dimerization interface analysis
Hi Andreas, This maybe a little ott, but the Rosetta suite of modelling programs will do docking with some minimisation and side chain optimisation. You can also enforce symmetry. http://www.rosettacommons.org/ http://depts.washington.edu/bakerpg/ It is free to academics and runs on most platforms. Hope this helps, Dave On 29/11/2007, Andreas Förster [EMAIL PROTECTED] wrote: Dear all, Karen question reminded me that I have one also. I study a protein that homodimerizes via a long helix. A number of homologs exist. They all dimerize, but the structure is only known of the first. Homology is high enough that I can easily thread the homologs' sequences onto the structure. How do I go about analyzing the new dimerization interfaces? Before having Pisa have a go, I'd like to do some sort of minimization to allow for wiggling of one helix with respect to the other and rotamerization of side chains. What I'm ultimately interested in is which homologs are likely to form heterooligomers. There is some experimental evidence for that. I'm grateful for suggestions. Andreas -- Andreas Förster Imperial College London https://wasatch.biochem.utah.edu/~andreas -- David C. Briggs PhD Father Crystallographer http://personalpages.manchester.ac.uk/staff/David.C.Briggs/ AIM ID: dbassophile
Re: [ccp4bb] Protein interface prediction tool?
PISA gives a good analysis of a known interface, but won't predict it from scratch. So basically you need a protein-protein docking program of which there are several: 3DDock, gramm, zdock, etc, etc There's a review in G.R.Smith and MJE Sternberg, Curr Opion Struct Biol, 12, 28 (2002) - obviously a little old now. See also the CAPRI assessment http://capri.ebi.ac.uk/ These methods will give you a surfeit of predictions, the fun is in choosing the one you like, e.g. using tools like PISA HTH Martyn On Thu, 2007-11-29 at 12:47 +, Andreas Förster wrote: Hey Karen, Pisa analyzes oligomerization interfaces. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Andreas karen yates wrote: Hi, I would like to find a bioinformatic tool that will allow me to predict the dimerisation interface of a protein. A structural model has been generated, and it is known to exist as a homo-dimer. Does anyone know of a suitable program? Thank you for your help. Karen This message was sent using IMP, the Internet Messaging Program. -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] PhD in GPCR Signalling
PhD in GPCR Signalling In my laboratory at the MRC Laboratory of Molecular Biology there are PhD opportunities in structural biology of G protein coupled receptor (GPCR) signalling. We have outstanding expertise in 2D and 3D crystallisation of GPCRs. We are working on the structure of GPCRs and on GPCR signalling complexes with electron microscopy and micro crystallography. This year we have solved the first structure of a recombinant GPCR Standfuss, J., et al. (2007) Crystal structure of a thermally stable rhodopsin mutant. J Mol Biol 372, 1179-1188 And in collaboration with Brian Kobilka we have solved the first structure of a Human beta 2 adrenergic receptor in complex with an antibody fragment. Rasmussen, S.G., et al. (2007) Crystal structure of the human beta(2) adrenergic G-protein-coupled receptor. Nature Nature 450, 383-387 Home Page: http://www2.mrc-lmb.cam.ac.uk/SS/Schertler_G/ Application deadlines: - EU/overseas application deadline: 14th December 2007 - UK application deadline: 4th January 2008 - LMB Cambridge Scholarship nomination deadline: 21st December 2007 Link LMB Funding http://www2.mrc-lmb.cam.ac.uk/projects/PhD_funding.html There are many more opportunities at the MRC Laboratory of Molecular Biology in other subject areas. You can informally contact me directly. Dr. Gebhard F. X. Schertler Senior Scientist and Group Leader MRC Laboratory of Molecular Biology Cambridge CB2 0QH tel 0044 1223 402328 fax 0044 1223 213556 e-mail [EMAIL PROTECTED] web http://www2.mrc-lmb.cam.ac.uk/SS/Schertler_G/
[ccp4bb] HHMI X-ray lab manager/Research Scientist Job
To all interested parties: A Research Scientist / X-ray lab manager position in the lab of Tom Cech in Boulder, Colorado is open. Job Description: The Howard Hughes Medical Institute, a leading biomedical research organization, is seeking an experienced scientist to manage our X-ray crystallography facility at the Cech research laboratory at the University of Colorado campus in Boulder. The facility is equipped with two Rigaku generators and R-Axis IV++ detectors for data collection, a linux cluster, and Macintosh computers for calculations and graphics, and a Fluidigm microfluidics crystallizer. The successful candidate will (1) Carry out routine maintenance on these instruments and coordinate service under service contracts; (2) perform routine Unix system administration and crystallographic software management; (3) provide basic training in the use of x-ray crystallographic equipment and software to users; and (4) engage in independent or collaborative research. Preferred qualifications include a Ph.D. degree in an appropriate field of science or technology, and three years of experience in a Research Specialist level position. Previous experience in Unix/Linux system administration and routine maintenance of crystallography hardware is essential. HHMI offers an excellent salary and comprehensive benefits package. Interested candidates please forward a statement of interest, CV, publications and references by December 30, 2007 to Ms. Robbie Haywood Oglesby, Administrative Assistant, 1200 Moursund Ave S101, Houston, Texas 77030 or e-mail [EMAIL PROTECTED] (Include Research Specialist - Cech Laboratory in the subject line of your e-mail). Marcelo C. Sousa, Ph.D. Department of Chemistry and Biochemistry Cristol Chemistry Building. Room 100 215 UCB University of Colorado at Boulder Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 5894
Re: [ccp4bb] Protein interface prediction tool?
Karen, MolSoft offers a free online tool that predicts protein-protein interfaces using our ICM software. http://www.molsoft.com/oda.cgi more information here: http://www.molsoft.com/oda.html Fernandez-Recio, J., Totrov, M., Skorodumov, C., Abagyan, R.Optimal Docking Area: A New Method for Predicting Protein-Protein Interaction Sites. Proteins 57:400-13 Thanks, Andy karen yates wrote: Hi, I would like to find a bioinformatic tool that will allow me to predict the dimerisation interface of a protein. A structural model has been generated, and it is known to exist as a homo-dimer. Does anyone know of a suitable program? Thank you for your help. Karen This message was sent using IMP, the Internet Messaging Program. -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com
Re: [ccp4bb] S-S in EC
Nonredundant summary - thx to all submitters: 1) disulfide was often present even after expression in a normal BL21 strain 2) try OrigamiB (DE3), Rosetta-Gami 2 from Novagen, are codon optimized and have mutations in the thiorodoxin reductase and glutathione reductase genes - expressing from pET32 vectors which contain a thioredoxin fusion tag - extra purification steps are generally needed to remove the thiorodoxin after cleavage of the fusion tag - level of expression achieved was not very impressive for E. coli, but enough to work with for structural studies - generally human, extracellular proteins - as always, protein dependent - Origami strains are somewhat slow growing and sick-seeming do not grow to very high densities and have to be coddled somewhat - They grow well enough in auto-induction media - grow to OD around 1.0-1.1 at 37, cool flasks in ice bath to 20, induce o/n with 30 uM IPTG at 18°C. - some success with periplasmic export for disulfide bridge formation using the OmpA leader sequence (not the PelB leader from the pET plasmids) 3) used the AD494 (trx) strain with good results 4) Tuner strain (also Novagen) and low levels of IPTG to induce expression - led to expression of a protein with one disulphide bridge 5) try pichia. br -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Wednesday, November 28, 2007 2:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] S-S in EC Dear All, I need to express a mammalian protein with S-S bridges and would hope to talk off-board with a person who knows about thioredoxin strains ect that might work. Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
[ccp4bb] Finding Chlorine =)
Dear all, I am refining two structures which have in the active site a ligand containing a covalent bond between a carbon and a chlorine atom. I collected the data at APS, SERCAT ID-22. Because of radiation damage I tried different occupancy values for the chlorine atom and structure number #1 is best with occupancy 0.2 while structure #2 seems to be happy with occupancy 0 (occupancy for the rest of the ligand is 1). I checked by mass spec if my compound has the molecular weight expected with a chlorine atom and it does, so the original compound was correct. Can radiation damage make the chlorine completely disappear? Do the different occupancy values I get depend also on the resolution? In fact: Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%) Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%) When I make the figures for publication, do I draw the ligand with or without chlorine? Thanks, Eli =) -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Finding Chlorine =)
Thank you for all the answers I am starting to get! In the meantime, could I please also ask you to suggest to me papers that would be a good reference to put in my publication? Thank you again! Eli =) On Thu, November 29, 2007 4:21 pm, Fischmann, Thierry wrote: Dear Eli, I work in a pharmaceutical company and go through many diverse compounds. My extensive experience with Br and Cl is that they easily get cleaved by X-ray. I've done a lot of experiments to address the problem: radical scavengers (fail: it does not look like the process is radical-mediated), energy dependence (fails: in fact cleavage occurs at the home Cu 1.54Å source), and fast data collection (success at the expense of data quality, but often mandatory). Cleavage happens much more readily if the halogen is exposed to solvent. In fact I have the ultimate proof that this is a determinant factor: a chiral compound which changes binding orientation when the chirality is inversed, and the halogen either exposed to solvent or buried depending on chirality. That atom is connected to a non-chiral, planar moiety, therefore its chemical environment is the same in each enantiomer. However cleavage is very fast in the solvent-exposed conformation, and very slow in the opposite orientation. Solutions: - Collect your data very quickly (example: after running a strategy, 1 second exposure for 1 degree sweep at the synchrotron, for a total sweep of 100 deg). The cleavage is clearly dose-dependent. - Re-scale your data after discarding data collected at the end. Often (but not always) these data add redundancy but do little to completeness. Try to discard as much data as possible while keeping the completeness reasonable. I wouldn't be surprised that the #1 structure would do much better in terms of Cl occupancy if you could get by with 50% of the data. #2 may be a more tricky case. As far as publication is concerned, I wouldn't show the Cl for #2, but I would show it for #1 if there is no indication that the binding pose has moved due to cleavage. That is the case for my compounds. Good luck! Thierry -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sabini, Elisabetta Sent: Thursday, November 29, 2007 04:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Finding Chlorine =) Dear all, I am refining two structures which have in the active site a ligand containing a covalent bond between a carbon and a chlorine atom. I collected the data at APS, SERCAT ID-22. Because of radiation damage I tried different occupancy values for the chlorine atom and structure number #1 is best with occupancy 0.2 while structure #2 seems to be happy with occupancy 0 (occupancy for the rest of the ligand is 1). I checked by mass spec if my compound has the molecular weight expected with a chlorine atom and it does, so the original compound was correct. Can radiation damage make the chlorine completely disappear? Do the different occupancy values I get depend also on the resolution? In fact: Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%) Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%) When I make the figures for publication, do I draw the ligand with or without chlorine? Thanks, Eli =) -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] * This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete. -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Finding Chlorine =)
Dear Elisabetta, Which program did you use for refinement? If you used REFMAC, the atomic scattering factors are internally coded for copper radiation, and the resulting electron density map after refinement may be much lower for halide atoms than it should be! It is a known REFMAC issue. Tadeusz Sabini, Elisabetta [EMAIL PROTECTED] Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 29-Nov-2007 21:40 Please respond to Sabini, Elisabetta [EMAIL PROTECTED] To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] Finding Chlorine =) Dear all, I am refining two structures which have in the active site a ligand containing a covalent bond between a carbon and a chlorine atom. I collected the data at APS, SERCAT ID-22. Because of radiation damage I tried different occupancy values for the chlorine atom and structure number #1 is best with occupancy 0.2 while structure #2 seems to be happy with occupancy 0 (occupancy for the rest of the ligand is 1). I checked by mass spec if my compound has the molecular weight expected with a chlorine atom and it does, so the original compound was correct. Can radiation damage make the chlorine completely disappear? Do the different occupancy values I get depend also on the resolution? In fact: Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%) Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%) When I make the figures for publication, do I draw the ligand with or without chlorine? Thanks, Eli =) -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] --- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ---
Re: [ccp4bb] Finding Chlorine =)
Another question: since during data collection the chlorine disappears, can the residues surrounding the chlorine adjust their position to compensate for the vanishing of the atom? Can the ligand move? Do things move during data collection? Meaning, can I describe what I see in my structure as a structure that have in its active site a ligand with a chlorineeven if it is really not there? ...but it was there during crystal growth...? Thanks again, Eli PS: I will read your answers tomorrow! GRAZIE GRAZIE!!! On Thu, November 29, 2007 5:04 pm, Sabini, Elisabetta wrote: Thank you for all the answers I am starting to get! In the meantime, could I please also ask you to suggest to me papers that would be a good reference to put in my publication? Thank you again! Eli =) On Thu, November 29, 2007 4:21 pm, Fischmann, Thierry wrote: Dear Eli, I work in a pharmaceutical company and go through many diverse compounds. My extensive experience with Br and Cl is that they easily get cleaved by X-ray. I've done a lot of experiments to address the problem: radical scavengers (fail: it does not look like the process is radical-mediated), energy dependence (fails: in fact cleavage occurs at the home Cu 1.54Å source), and fast data collection (success at the expense of data quality, but often mandatory). Cleavage happens much more readily if the halogen is exposed to solvent. In fact I have the ultimate proof that this is a determinant factor: a chiral compound which changes binding orientation when the chirality is inversed, and the halogen either exposed to solvent or buried depending on chirality. That atom is connected to a non-chiral, planar moiety, therefore its chemical environment is the same in each enantiomer. However cleavage is very fast in the solvent-exposed conformation, and very slow in the opposite orientation. Solutions: -Collect your data very quickly (example: after running a strategy, 1 second exposure for 1 degree sweep at the synchrotron, for a total sweep of 100 deg). The cleavage is clearly dose-dependent. -Re-scale your data after discarding data collected at the end. Often (but not always) these data add redundancy but do little to completeness. Try to discard as much data as possible while keeping the completeness reasonable. I wouldn't be surprised that the #1 structure would do much better in terms of Cl occupancy if you could get by with 50% of the data. #2 may be a more tricky case. As far as publication is concerned, I wouldn't show the Cl for #2, but I would show it for #1 if there is no indication that the binding pose has moved due to cleavage. That is the case for my compounds. Good luck! Thierry -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sabini, Elisabetta Sent: Thursday, November 29, 2007 04:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Finding Chlorine =) Dear all, I am refining two structures which have in the active site a ligand containing a covalent bond between a carbon and a chlorine atom. I collected the data at APS, SERCAT ID-22. Because of radiation damage I tried different occupancy values for the chlorine atom and structure number #1 is best with occupancy 0.2 while structure #2 seems to be happy with occupancy 0 (occupancy for the rest of the ligand is 1). I checked by mass spec if my compound has the molecular weight expected with a chlorine atom and it does, so the original compound was correct. Can radiation damage make the chlorine completely disappear? Do the different occupancy values I get depend also on the resolution? In fact: Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%) Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%) When I make the figures for publication, do I draw the ligand with or without chlorine? Thanks, Eli =) -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] * This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete. -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago
Re: [ccp4bb] Finding Chlorine =)
But you can change it with the keyword anomolous formfactor element f' f'' Where f' and f'' correspond to values for a given wavelength. See for details: http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html Internally yes. It is CuKa. Garib On 29 Nov 2007, at 23:19, Tadeusz Skarzynski wrote: Dear Elisabetta, Which program did you use for refinement? If you used REFMAC, the atomic scattering factors are internally coded for copper radiation, and the resulting electron density map after refinement may be much lower for halide atoms than it should be! It is a known REFMAC issue. Tadeusz Sabini, Elisabetta [EMAIL PROTECTED] Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 29-Nov-2007 21:40 Please respond to Sabini, Elisabetta [EMAIL PROTECTED] To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] Finding Chlorine =) Dear all, I am refining two structures which have in the active site a ligand containing a covalent bond between a carbon and a chlorine atom. I collected the data at APS, SERCAT ID-22. Because of radiation damage I tried different occupancy values for the chlorine atom and structure number #1 is best with occupancy 0.2 while structure #2 seems to be happy with occupancy 0 (occupancy for the rest of the ligand is 1). I checked by mass spec if my compound has the molecular weight expected with a chlorine atom and it does, so the original compound was correct. Can radiation damage make the chlorine completely disappear? Do the different occupancy values I get depend also on the resolution? In fact: Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%) Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%) When I make the figures for publication, do I draw the ligand with or without chlorine? Thanks, Eli =) -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] --- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ---
