[ccp4bb] Postdoctoral Felloship available
A postdoctoral opportunity exists in the laboratory of Richard Baxter at the Temple University School of Medicine in Philadelphia to investigate the structure and function of complement-like proteins in insects, their roles in immunity, development, and the transmission of infectious diseases. You will join an interdisciplinary group using biochemistry, biophysics, structural biology, and cell-based assays in collaboration with experts at the organismal level. Your objective will be to elucidate novel molecular mechanisms of immunity, and new connections between invertebrate and vertebrate immune responses, that can be leveraged to predict and disrupt disease. For recent publications and current projects, please visit http://sites.temple.edu/baxterlab Applicants should have a Ph.D. in chemistry, biochemistry, biophysics, biochemistry or related disciplines, a record of peer-reviewed publication, and familiarity with standard laboratory techniques of molecular cloning, protein expression and purification, and structural techniques such as x-ray crystallography, electron microscopy, small angle x-ray scattering, and/or mass spectrometry. Interested applicants please send (i) cover letter, (ii) curriculum vitae, and (iii) name and contact information for three references to Prof. Richard Baxter by email: rbax...@temple.edu.
[ccp4bb] Postdoctoral Positions available - Baxter Laboratory
Opportunities exist for up to two postdoctoral scholars, available August 1, 2017, to investigate innate immunity in insects, its role in development, and in the transmission of infectious diseases. You will join an interdisciplinary group using biochemistry, biophysics, structural biology, and cell-based assays in collaboration with experts at the organismal level. Your objective will be to elucidate novel molecular mechanisms of immunity, and new connections between invertebrate and human immune responses, that can be leveraged to predict and disrupt disease transmission. For more information, visit http://baxterlab.yale.edu. Applicants should have a Ph.D. in chemistry, biophysics, biochemistry, molecular biology, or related discipline, record of peer-reviewed publication, and familiarity with standard laboratory techniques such as PCR/molecular biology, protein expression and purification, and analysis of proteins and nucleic acids by spectroscopy, electrophoresis, etc. The following skills are of specific interest: Project 1: Structural analysis of complement-like proteins in the immune response of Anopheles gambiae to Plasmodium infection. Expertise in structural techniques such as x-ray crystallography, electron microscopy, small angle x-ray scattering, and/or mass-spectrometry techniques for quantitation. Experience in eukaryotic cell culture, especially baculovirus expression vector systems (BEVS). Project 2: Functional analysis of Drosophila thioester-containing proteins in immunity and development. Expertise in cell-based assays such as flow cytometry, microscopy, RNAi knockdown and qPCR, Analysis of protein-protein interactions by proteomics/mass-spectrometry. Experience in eukaryotic cell culture, including genetic manipulation or antibody production. Interested applicants please send (i) cover letter, (ii) curriculum vitae, and (iii) name and contact information for three references to Prof. Richard Baxter by email: richard.bax...@yale.edu.
[ccp4bb] Postdoctoral Position studying complement-like immunity in mosquitoes
A postdoctoral position is available in the laboratory of Prof. Richard Baxter at Yale University (baxterlab.yale.edu). The successful candidate will address structural and mechanistic questions regarding the innate immune response of the malaria vector *Anopheles gambiae*. They will join a research group that combines biophysical techniques such as x-ray crystallography, small-angle x-ray scattering with biochemistry, chemical and cell biology. The laboratory is located in the Kline Chemistry Laboratory (newly renovated June 2014) with access to in-house x-ray diffraction and biophysical instrumentation, cryo-EM facility and expanding facilities for proteomics and high-throughput biology at the Yale Keck Center and the Yale West Campus. A PhD in chemistry, biochemistry, biophysics or other relevant discipline is required. Experience with macromolecular crystallography, SAXS, electron microscopy or mass spectrometry is preferred, experience in vector biology or host-pathogen interactions is a plus. Interested applicants please submit a cover letter, resume and contact information for three references to Richard Baxter, Tel: +1 203 432 9576, 225 Prospect Street, PO Box 208107, New Haven CT 06511, or email richard.bax...@yale.edu
[ccp4bb] Research Support Specialist - Yale University
Dear All, For any small molecule crystallographers who may read this board, the Yale Chemistry Biophysical Instrumentation Center has a position available. Besides performing service crystallography the successful applicant will cooperate with other CBIC staff in the maintenance of analytical equipment and some other duties. To view the opening visit Yale's external Careers site: http://www.yale.edu/hronline/careers/application/external/index.html Search for STARS Requisition number 20613BR Best wishes, Richard Baxter -- Asst. Prof. in Chemistry = Yale University PO Box 208107 New Haven, CT 06520-8107 Tel: +1 203 432 9576 Fax: +1 203 432 6144 www.baxterlab.org =
[ccp4bb] refining beta peptides
Dear All, Looking to refine a beta-peptide structure (2 A resolution). Any advice on use of Refmac, Phenix, SHELX for this, are they in the dicionary? Thanks a lot. Richard -- Asst. Prof. in Chemistry = Yale University PO Box 208107 New Haven, CT 06520-8107 Tel: +1 203 432 9576 Fax: +1 203 432 6144 www.baxterlab.org =
[ccp4bb] Postdoctoral Position Available
Dear All, A position is available for a postdoctoral fellow to pursue structural and functional studies of proteins involved in the innate immune response of Anopheles gambiae to malaria infection. The successful candidate will be part of a new research group combining biophysical techniques such as x-ray crystallography and small-angle x-ray scattering with biochemical characterization and in vivo validation through collaborative studies. The position offers access to in-house x-ray diffraction facilities within the Chemistry Dept., numerous local core facilities, synchrotron access at NSLS and APS, and expanding opportunities for high-throughput biology at Yale's West Campus facility. Please email a cover letter, resume and contact information for three references to richard.bax...@yale.edu, or visit http://baxterlab.sites.yale.edu for further contact information. For scientific details see the following publications: Baxter, R.H.G., et. al (2010) A heterodimeric complex of the LRR proteins LRIM1 and APL1C regulates complement-like immunity in Anopheles gambiae PNAS 107, 16817-16822. [doi:10.1073/pnas.1010575107, PMID:20826443] Fraiture, M. et. al (2009) Two mosquito LRR proteins function as complement control factors in the TEP1-mediated killing of Plasmodium Cell Host Microbe 5, 273-284. [doi:10.1016/j.chom.2009.01.005, PMID 19286136] Baxter, R.H.G. et. al (2007) Structural basis for conserved complement factor-like function in the antimalarial protein TEP1 PNAS 104, 11615-11620. [doi:10.1073/pnas.0704967104, PMID:17606907]
Re: [ccp4bb] The importance of USING our validation tools
Dear All, Without passing any judgement on the veracity of C3b structure 2hr0, I note that the Ca RMSD of this structure with C3 structure 2a73 was unusually low, compared to the RMSD of 2a73 to the related entries 2a74 and 2i07 by the same group, bovine C3 structure 2b39 and C3b and C3c structures 2ice and 2icef. If one took a high resolution structure as a molecular replacement solution of a new structure at lower resolution this might be expected, but not vice versa? As to whether the structures problem arise from malfeasance or neglect, I do not understand why the journal did not require the raw images be made available given the evidence presented against the published data, isn't that what is done in other fields when such issues are raised? Isn't it more practical to make the availability of raw data upon request a requirement of publication more practical than trying to set up a vast repository of images when submission to that repository is still a matter of choice? I have several questions regarding the reply that I would like to hear an answer to, perhaps Todd can help obtain them: 1. Could the statement Statistical disorder resulting in apparent 'gaps' in the lattice has been observed for other proteins not be referenced by citation to numerous deposited structures if they indeed exist? 2. I was not convinced that the Z-scores of the PHASER solutions were significant, shouldn't they be greater than 6.0? It didn't look like density at 0.7 sigma was contiguous over the main chain. 3. Can the domain suggested to fill the void in the asymmetric unit be a contaminant when it must be present in stoichiometric ratio in order to provide lattice contacts? Why not present a SDS/PAGE gel of a redissolved crystal, surely that domain would show up. 3. I don't understand why the statement Bulk-solvent modelling is contentious, making many refinements necessary to constrain parameters to obtain acceptable values was considered an acceptable response to the question of the low resolution data. Whether one chooses to include low-resolution data with bulk solvent modelling or to truncate the low res data is a separate issue from the physical effect of solvent on intensities at low resolution. One point in the reply that seemed reasonable is the issue of B-factor variation, because the deposited C3 structures do exhibit a wide range in the average B, also resolution, and whether TLS refinement was used and how heavily restraints were set. However, that does not really address the issue of seemingly random coil without other contacts having such great contours at 2.5 sigma. I would look forward to learning from people with more experience on these matters. sincerely, Richard Baxter On Thu, 2007-08-16 at 10:11, Green, Todd wrote: Hello all, I started to write a response to this thread yesterday. I thought the title was great even the content of Eleanor's email was very helpful. What I didn't like was the indictment in the next to last paragraph. This has been followed up with the word fabrication by others. No one knows definitively if this was fabricated. You have your suspicions, but you don't know. Fabrication suggests malicious wrong-doing. I actually don't think this was the case. I'm probably a bit biased because the work comes from an office down the hall from my own. I'd like to think that if the structure is wrong that it could be chalked up to inexperience rather than malice. To me, this scenario of inexperience seems like one that could become more and more prevalent as our field opens up to more and more scientists doing structural work who are not dedicated crystallographers. Having said that, I think Eleanor started an extremely useful thread as a way of avoiding the pitfalls of crystallography whether you are a novice or an expert. There's no question that this board is the best way to advance one's knowledge of crystallography. I actually gave a homework assignment that was simply to sign up for the ccp4bb. In reference to the previously mentioned work, I'd also like to hear discussion concurring or not the response letter some of which seems plausible to me. I hope I don't ruffle anyones feathers by my email, but I just thought that it should be said. Cheers- Todd -Original Message- From: CCP4 bulletin board on behalf of Randy J. Read Sent: Thu 8/16/2007 8:22 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] The importance of USING our validation tools On Aug 16 2007, Eleanor Dodson wrote: The weighting in REFMAC is a function of SigmA ( plotted in log file). For this example it will be nearly 1 for all resolutions ranges so the weights are pretty constant. There is also a contribution from the experimental sigma, which in this case seems to be proportional to |F| Originally I expected that the publication of our Brief Communication in Nature would stimulate a lot of discussion on the bulletin board, but clearly
