[ccp4bb] (ccp4bb) Bayer Healthcare's Berlin based Pharma business is looking for a Research Scientist (m/f) – Protein Crystallography
Bayer Healthcare's Berlin based Pharma business is looking for a Research Scientist (m/f) – Protein Crystallography Bayer Healthcare's Berlin based Pharma business, which generated sales of EUR 11.7 billion in 2006, is one of the ten largest specialty pharmaceuticals companies in the world. With outstanding research work in its six key therapeutic areas – Diagnostic Imaging, Hematology/Cardiology, Oncology, Primary Care, Specialty Therapeutics and Women’s Healthcare. Our company plays a crucial role in promoting medical progress. Your Job as a research scientist in structural biology (protein crystallographer) in Berlin comprise state-of-the-art crystallisation, data collection and structure determination of protein-ligand complexes as well as their interpretation, assessment and documentation, including in-depth characterization of binding niches. Generation of homology models is also part of the responsibilities. The tasks also involve communication and discussion of the results in multi-disciplinary drug discovery teams. Your qualifications includes PhD in structural biology, or related sciences (biochemistry, chemistry) with a bioinformatics background. Your expertise is in protein X-ray crystallography with an emphasis on experimental phasing techniques. Knowledge in protein purification and/or small molecules crystallography is an advantage. Your job experience is more than 3 years in modern crystallisation techniques and X-ray structure determinations of a variety of protein classes. Good communication skills and excellent spoken and written English are essential together with efficient working methods and the ability to think analytically. The ability to work as part of a team, a sense of responsibility and organizational talent round off your profile. Your application should be submitted online along with enclosures such as a letter of introduction, your CV and references. Contact FON: +49 30 468 12357 Please apply here: Bayer
[ccp4bb] Nearly perfect twinned data????
Hi all, We have collected few X-ray data sets for a protein-RNA complex to resolutions of 3.2-3.5A. While processing the data using HKL2000, we have obtained following distortion index consistently: primitive cubic 19.16% 127.98 74.67 130.85 74.57 85.00 73.91 111.17 111.17 111.17 90.00 90.00 90.00 I centred cubic 24.26% 132.28 189.90 127.98 120.33 85.97 120.47 150.05 150.05 150.05 90.00 90.00 90.00 F centred cubic 22.17% 177.47 190.41 189.90 46.24 90.79 91.90 185.93 185.93 185.93 90.00 90.00 90.00 primitive rhombohedral 16.32% 130.85 129.06 174.88 131.21 133.20 86.12 144.93 144.93 144.93 116.85 116.85 116.85 229.30 229.30 74.67 90.00 90.00 120.00 primitive hexagonal 15.40%130.85 127.98 74.67 106.09 74.57 95.00 129.41 129.41 74.67 90.00 90.00 120.00 primitive tetragonal 9.40% 127.98 130.85 74.67 74.57 106.09 95.00 129.41 129.41 74.67 90.00 90.00 90.00 I centred tetragonal 0.91% 177.47 174.88 74.67 90.21 88.59 91.47 176.18 176.18 74.67 90.00 90.00 90.00 primitive orthorhombic 9.38% 74.67 127.98 130.85 85.00 105.43 106.09 74.67 127.98 130.85 90.00 90.00 90.00 C centred orthorhombic 6.53% 74.67 245.95 130.85 89.44 105.43 89.13 74.67 245.95 130.85 90.00 90.00 90.00 I centred orthorhombic 0.84%74.67 174.88 177.47 88.53 91.41 90.21 74.67 174.88 177.47 90.00 90.00 90.00 F centred orthorhombic 0.68%74.67 245.95 252.32 89.16 88.86 89.13 74.67 245.95 252.32 90.00 90.00 90.00 primitive monoclinic 6.52% 74.67 130.85 127.98 95.00 106.09 74.57 74.67 130.85 127.98 90.00 106.09 90.00 C centred monoclinic 0.49% 74.67 245.95 130.85 89.44 105.43 89.13 74.67 245.95 130.85 90.00 105.43 90.00 primitive triclinic 0.00% 74.67 127.98 130.85 85.00 74.57 73.91 As you see, distortion index table indicates I centered tetragonal, I centered orthorhombic, F centered orthorhombic, C centered monoclinic and triclinic as possible Bravais lattices. Data processed in I centered tetragonal gives low Rmerge in all the possible space groups namely I4, I41, I422 and even I4122. Other space groups in lower symmetry lattices also gave low R merge values (around 6% in most of the cases). Since we have not been able to obtain a solution in any of the space group from I centered tetragonal to triclinic (I4, I4122, I222, C2 and even P1) using Se-SAD, we decided to check the data for any intrinsic problem such as twinning. Cumulative intensity distribution calculated using scalepack2mtz shows no sign of twinning. However, data processed in I4 shows nearly a perfect twin (twin fraction=0.489 with twin operator 100 0-10 00-1) in Yeates server whereas SFcheck indicates a twin fraction of 0.431 with twin operator –h,+k,-l. Data processed in I4122, I222, C2 and P1 doesn't show any twinning due to absence of any twin laws for these space groups. Now my question is: - Are data showing low Rmerge value in I4122 due to nearly perfect twin in space group I4? - Why cumulative intensity distribution shows a normal pattern for the data where as Yeates server and SFcheck indicates nearly a perfect twin? Why Yeates server and SFCheck shows different twin fraction and twin operator? - Is it possible to detwin this data and use it for structure solution? Thank you for reading till this line and I am sorry for such a long mail. I hope I haven't made any mistake at any stage. I really need your valuable suggestions to solve this problem. Regards Joe
[ccp4bb] Positions available at RCSB PDB- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST
The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for researchers and students interested in structural biology. At its center is the PDB archive – the sole international repository for the 3-dimensional structure data of biological macromolecules. These structures hold significant promise for the pharmaceutical and biotechnology industries in the search for new drugs and in efforts to understand the mysteries of human disease. The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely and efficient way possible to facilitate new discoveries and scientific advances. The RCSB processes, stores, and disseminates these important data, and develops the software tools needed to assist users in depositing and accessing structural information. The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has two openings for a Biochemical Information Annotation Specialists to curate and standardize macromolecular structures for distribution in the PDB archive. The annotation specialists validate, annotate, and release structural entries in PDB archive. The annotation specialists also communicate daily with members of the deposition community. The position is an academic position with state benefit. The salary is compatible with faculty level. A background in macromolecular crystallography or small molecule crystallography or cryo-electron microscopy is a strong advantage. Biological chemistry (PhD, MS) is required. Experience with linux computer systems, biological databases is preferred. The successful candidate should be self-motivated, pay close attention to detail, possess strong written and oral communication skills, and meet deadlines. These positions offer the opportunity to participate in an exciting project with significant impact on the scientific community. Please send resume (pdf preferred) to Dr. Helen M. Berman at [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Re: [ccp4bb] Nearly perfect twinned data????
As you see, distortion index table indicates I centered tetragonal, I centered orthorhombic, F centered orthorhombic, C centered monoclinic and triclinic as possible Bravais lattices. Data processed in I centered tetragonal gives low Rmerge in all the possible space groups namely I4, I41, I422 and even I4122. Other space groups in lower symmetry lattices also gave low R merge values (around 6% in most of the cases). If it processes nicely in I422, it will also in subgroups of I422 (sub as I4, I222, various choices of C2 and of course P1). Since we have not been able to obtain a solution in any of the space group from I centered tetragonal to triclinic (I4, I4122, I222, C2 and even P1) using Se-SAD, we decided to check the data for any intrinsic problem such as twinning. Do you have any anomalous signal? snap Now my question is: - Are data showing low Rmerge value in I4122 due to nearly perfect twin in space group I4? That is possible, but seems unlikely. - Why cumulative intensity distribution shows a normal pattern for the data where as Yeates server and SFcheck indicates nearly a perfect twin? Why Yeates server and SFCheck shows different twin fraction and twin operator? Twin fraction estimates rely on correlations between twin related intensities. If you process yuor data in a spacegroup that is too low, you will see that 1. You have twin laws available for your crystal symmetry 2. You have strong correlations between twin related reflections In both cases, the cause is the that you have wrong symmetry. Twinning analyses should take into account the presence of wrong symmetry. If that is not done, question like this come up. Furthermore, the yeates server unfortunately doesn't deal with pseudo merohedral twinning. The differences in twin operators is due to the crystal symmetry: the operators listed are related by the symmetry of I4. The difference in twin fraction is due to difference s in data cuts and resolution limits I suppose. I highly recommend using phenix.xtriage (for obvious reasons) to give you a relatively clear picture of what is going on. Get it from the latest phenix release. usage is straightforward. - Is it possible to detwin this data and use it for structure solution? I guess you first want to make sure that your experimental data has any anomalous signal at all before your blame twinning to be the reason that you cannot solve your structure. HTH P
[ccp4bb] Scientist Positions at the Centre of Free Electron Laser Science in Hamburg
Scientist Positions within the Advanced Study Group of the Max Planck Society at the Centre of Free Electron Laser Science in Hamburg The Advanced Study Group (ASG) funded by the Max Planck Society (MPG) is part of the Centre for Free Electron Laser Science (CFEL) presently being established in Hamburg (http://hasylab.desy.de/science/cfel/index_eng.html). The ASG shall support research activities of groups within the Max-Planck-Society at 4th generation Free Electron Laser (FEL) light sources such as FLASH in Hamburg and LCLS in Stanford. Applications are invited for two scientist positions, located at DESY, to establish in Hamburg a fast-laser and pulsed x-ray laboratory for the preparation of MPG-FEL experiments, to operate and maintain single-photon counting x-ray pixel CCDs developed from the Max-Planck semiconductor laboratory. They are supported by two further scientists, two technicians and students. Specifically, we are looking for researchers experienced in (1) time-resolved diffraction methods. The successful candidate should have a strong background in physics, chemistry or biophysics or crystallography. Experience in diffraction experiments at FEL, SPPS or synchrotrons sources, or, alternatively, in ultra-fast x-ray science based on table top pulsed x-ray sources, are of advantage (2) x-ray spectroscopy and coherent scattering. The successful candidate should have a strong background in x-ray spectroscopy, operation of monochromators at FELs or synchrotrons and x-ray detection. Experience with CCD devises with FEL, SPPS or ESRF experiments and in coherent scattering are or advantage. This position is understood as a link between instrument developers and beamline scientists. We expect the successful candidates to interact collaboratively among a variety of disciplines. Apart from supporting experiments actively pursued within the ASG, independent research is encouraged. Remunerations are according to TVD (German civil service scale). The initial appointment will be for three years, with the possibility for a two-year extension. It is intended to have a long term perspective, given excellent performance and the continuation of funding by MPG within the CFEL. As an equal opportunity employer, the Max Planck Society seeks to increase the percentage of female employees in areas where they are under-represented. Qualified women are therefore strongly encouraged to apply. The Max Planck Society is also committed to employing more individuals with disabilities. We therefore actively encourage individuals with disabilities to apply. To apply, please send your CV including a brief description of your research / scientific interests, a list of publications, a copy of the most relevant publication, and names and email addresses of two referees either as email attachments or hard copy to: Prof. Dr. Joachim Ullrich <>Max-Planck-Institut fr Kernphysik Saupfercheckweg 1 D-69117 Heidelberg [EMAIL PROTECTED] Informal enquiries may be sent to Dr. Simone Techert ([EMAIL PROTECTED]) and Prof. Dr. Lothar Strder ([EMAIL PROTECTED]) for position 1 and 2, respectively. Deadline for applications is Dec 1st 2007, desired starting date as soon as possible.
[ccp4bb] Past CCP4 meeting on problem structures
Dear BB archivists, rumor has it that there was an early ccp4 meeting on problem structures and how to improve methods (with D. Eisenberg attending). If so, do we have proceedings of that available? I think they are archived somewhere on the Daresbury site but I can't find it. Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - It is not your aptitude but your attitude that determines your altitude. -
Re: [ccp4bb] Past CCP4 meeting on problem structures
Hi Bernhard You may be referring to the one I was involved in organising: http://epubs.cclrc.ac.uk/bitstream/946/DL-SCI-R28.pdf Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: 26 September 2007 19:38 To: CCP4BB@JISCMAIL.AC.UK Subject: Past CCP4 meeting on problem structures Dear BB archivists, rumor has it that there was an early ccp4 meeting on problem structures and how to improve methods (with D. Eisenberg attending). If so, do we have proceedings of that available? I think they are archived somewhere on the Daresbury site but I can't find it. Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - It is not your aptitude but your attitude that determines your altitude. - 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
