Re: [ccp4bb] Best compounds for heavy atom soaks
Hi All, A truly herculean response! Thanks everyone, I will process all of the information and come up with a strategy. Rhys
Re: [ccp4bb] Best compounds for heavy atom soaks
Hi Rhys, It's worth paying close attention to your crystallisation conditions as well - some heavy atom compounds will not be at all soluble in very alkaline (they'll form insoluble hydroxides) or phosphate/sulphate containing mother liquors. A very low pH may reduce the binding efficiency of some heavy atom compounds as well - many heavy atom compounds rely on having deprotonated side chains to interact with - if you are at pH 5 or lower, everything save your Asps and Glus are likely to be protonated and you'll perhaps have better luck with Lanthanides (or Uranyl salts). Good luck! Dave David C. Briggs PhD http://about.me/david_briggs On 16 January 2014 09:53, RHYS GRINTER r.grinte...@research.gla.ac.ukwrote: Hi All, A truly herculean response! Thanks everyone, I will process all of the information and come up with a strategy. Rhys
Re: [ccp4bb] Best compounds for heavy atom soaks
Hi John, Another way to screen for mercury derivatives. Rachelle vincent Chaptal vincent.chap...@ibcp.fr wrote: Hi Rhys, you already have a lot of suggestions to try. We all have our own reciepe for good derivatization, and this is due to the fact that we don't really understand what is going on. I can't explain why one HA binds to my protein while the other one doesn't, but I can visualize it and hence choose the good one. And i've observed this behavior with several proteins already. I would suggest that you try which HA is best for you, and use this specific one for your soaks. Testing different HA is quite easy and can be done simply by running a gel. you can try native-PAGE if your protein handles it, or we developped a technique on SDS-PAGE coupled with a fluorescence dye (http://www.ncbi.nlm.nih.gov/pubmed/20152903). Using these techniques, you can distinguish easily which HA binds to your protein (in the later case, free cysteines) and you will have big surprises. You can test concentration and derivatization time fitting your needs, you do this at your bench and have the result within an hour. It's worth investing the time in biochemistry before going to the synchrotron and processing lots of data to realize it wasn't the good HA and it won't bind to your protein... It won't garantee a non-mobile HA in the crystal, but at least you will try something that has more chances on working. Don't hesistate to contact me if you need more practical infos. Good luck Vincent On Jan 16, 2014, at 2:18 AM, RHYS GRINTER wrote: Hello message board, My group has some crystals of an interesting protein to take to the synchrotron in a couple of weeks. We won't be able to prepare and crystallise a SelMet derivative during that time period, but we have loads of crystals sitting around. The diffraction isn't great, we see maybe 3.5 at home but might be enough to get over the line. It will be a very difficult MR target, so we were thinking of soaking so crystals with heavy atomic compounds that we have lying around. I was wondering if people had any suggestions of compounds that people have used successfully for experimental phasing and maybe concentrations to use and soaking time. Cheers, Rhys -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr
Re: [ccp4bb] R-factors from SfCHECK versus R-factors from PHENIX
SFCHECK is a very quick and dirty report generator - On 15 January 2014 21:42, Pavel Afonine pafon...@gmail.com wrote: Hi Ursula, you will find answers here: http://www.phenix-online.org/papers/he5476_reprint.pdf Pavel On Wed, Jan 15, 2014 at 1:38 PM, Ursula Schulze-Gahmen uschulze-gah...@lbl.gov wrote: I am submitting a structure to the PDB database. The SfCHECK summary report provided by the PDB validation shows an R-factor for model vs structure factors of 0.32, while the R-factor from the refinement program PHENIX is 0.21. I am not familiar with SfCHECK, but I am puzzled how these programs can calculate such different R-factors. I would be thankful for some explanation. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 642 8766
[ccp4bb] Abstract Submission for BCA Spring Meeting 2014
Dear BCA members, The 2014 Spring BCA meeting is not far away now and the abstract submission deadline is fast approaching – 1 week remains! Abstracts can be submitted at: http://www.hg3.co.uk/bca/ The deadline for submissions is 9 am on Monday January 20th. This deadline applies to both oral and poster presentations and to both contributed and invited abstracts. The deadline cannot be extended. The theme of the meeting is Crystallography@100: Looking to the Future, Learning from the Past, and reflects the period of centenary celebration of the field of crystallography, marked by 2014 being designated the International year of Crystallography (IYCr) by UNESCO. The main meeting will be held at The University of Loughborough on April 8-10th, 2014, and features 13 symposia, the Bragg and Lonsdale lectures, 4 additional plenary lectures and 4 prize lectures for early career researchers. The meeting is preceded as usual, by the one-day Young Scientists Satellite Meeting (April 7-8th). Details of the meeting programme, as well as registration details, can be found on the BCA website at: http://crystallography.org.uk/bca-spring-meeting-7th-10th-april-2014/ I hope to see many of you at the meeting this year and look forward to seeing the abstracts flowing in. Best wishes Lee Brammer BCA 2014 Programme Chair Professor of Chemistry University of Sheffield
[ccp4bb] Docking model
Hi, I made one docking model of a protein complex by NMR and another one by modeling. I wanted to knowwhich software to useto minimize the energy (close contacts, H bonds, ...) best regards, Thomas. -- Thomas RORET BioMod Team Tel. 00 333 83 68 47 89 CRM2 UMR CNRS-UL 7036 Faculté des Sciences et Technologies BP 70239 54506 Vandoeuvre-les-Nancy
Re: [ccp4bb] Docking model
Hi Thomas, maybe you can try to use AMBER programs. http://ambermd.org/ I think these programs allow you to use different forcefield to minimise the energy of your model. Hope to Help Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Thomas RORET [thomas.ro...@univ-lorraine.fr] Envoyé : jeudi 16 janvier 2014 15:32 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Docking model Hi, I made one docking model of a protein complex by NMR and another one by modeling. I wanted to knowwhich software to useto minimize the energy (close contacts, H bonds, ...) best regards, Thomas. -- Thomas RORET BioMod Team Tel. 00 333 83 68 47 89 CRM2 UMR CNRS-UL 7036 Faculté des Sciences et Technologies BP 70239 54506 Vandoeuvre-les-Nancy
Re: [ccp4bb] determining best of alternative indexes with POINTLESS
Indeed that is a bug. I've never tried that combination before. I'll fix it Phil On 16 Jan 2014, at 20:32, wtempel wtem...@gmail.com wrote: Hello, using merged scalepack intensities and a reference MTZ file as inputs, I would like to prepare an MTZ of scalepack intensities reindexed so that the intensities optimally correspond to those in the reference MTZ file. Invoking POINTLESS with the CELL, SCAIN, HKLREF keywords results in CCP4MTZfile: open_read - File missing or corrupted:myscalepackoutput.sca hkl_merged_list: object not constructed Does pointless expect non-merged scalepack intensities, even though I assume the Laue group of the reference MTZ file? I could use no merge original index scalepack reflections were not that reflection file format lacking the unit cell dimensions. For simplicity and reliability, I would like to use an input file that provides both intensities and the corresponding cell dimensions. Can I achieve my goal by invoking POINTLESS differently. Could I provide merged reflections in MTZ format? Are there better approaches to my problem? Thank you for your consideration, Wolfram Tempel
Re: [ccp4bb] Best compounds for heavy atom soaks
A favorite resource is Bart Hazes' web page on heavy atom derivatives. http://homepage.usask.ca/~pag266/bart-hazes.html Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
[ccp4bb] Postdoctoral Position at UCSF - Structure of Receptor Tyrosine Kinases
UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF) POSTDOCTORAL POSITION, JURA LAB Structural studies of receptor tyrosine kinases A postdoctoral position in Receptor Tyrosine Kinase Structural Biology is available immediately for highly motivated individuals with a strong interest in structural studies of tyrosine kinase signaling in the lab of Prof. Natalia Jura at the University of California, San Francisco (UCSF). The individuals with the experience in electron microscopy are strongly encouraged to apply. The Jura Lab merges structural, biochemical, imaging and cell biology approaches to dissect the mechanism of multi-protein assemblies involved in receptor tyrosine kinase signaling at the plasma membrane. More information is available at the lab website: http://www.cvri.ucsf.edu/~jura The position offers ideal opportunities for an experienced structural biologist who would like to complement his or her expertise with other, diverse tools for understanding the molecular basis for regulation of growth signaling at the plasma membrane and general kinase activation mechanisms. The fellow will benefit from both the multidisciplinary environment in the lab and the highly collaborative UCSF community. The lab has extensive crystallographic and electron microscopy resources, including (as part of the UCSF crystallography group) two R-axis IV systems, a Tecnai TF20 electron microscope, and regular access to synchrotron beamline 8.3.1 at the nearby Advanced Light Source (ALS) in Berkeley. Candidates should have (or expect) a Ph.D. or M.D. and should have experience in protein purification, crystallization, and structure determination. Interested individuals should send a current CV to Prof. Natalia Jura at natalia.j...@ucsf.edumailto:natalia.j...@ucsf.edu _ -- Natalia Jura, Ph.D. Assistant Professor Cardiovascular Research Institute MC:3122 Department of Cellular and Molecular Pharmacology University of California San Francisco 555 Mission Bay Blvd South, Rm 452W San Francisco, CA 94158‐9001 Phone: 415 514 1133 Fax: 415 476 8173 Lab Website: http://www.cvri.ucsf.edu/~jura
