[ccp4bb] IMCA-CAT beam time is available for proprietary experiments
Dear Colleagues, The IMCA-CAT beamline at the Advanced Photon Source (APS) is continuing to operate and collect crystallography data during the current restricted-access operations at Argonne National Laboratory. Experiments are limited to (1) critical research related to COVID-19 or (2) critical proprietary research related to drug development. The current APS run cycle (2020-1) has been extended through May 31, 2020 in order to best provide structural biology data to fight COVID-19. The next APS run cycle (2020-2) has also been shifted and will now begin on June 10, 2020. All pharmaceutical companies and research entities conducting either COVID-19 related research or critical, proprietary research in drug discovery are invited to inquire about access to IMCA-CAT for beam time. All experiments must be either remote access or mail-in. IMCA-CAT is committed to accelerating drug discovery through synchrotron-based structural biology research. The insertion device beamline is optimized for delivering exceptional quality data, collecting data at high-throughput rates, and ensuring data security for proprietary experiments. Streamlined pathways for establishing proprietary agreements have been implemented for new industrial users to begin conducting experiments without delay. For more information about accessing IMCA-CAT, please contact Dr. Lisa Keefe (email is keefe [at] imca-cat.org). Work safely and stay healthy, Jesse Yoder -- Jesse Yoder, PhD Macromolecular Crystallographer IMCA-CAT | Argonne National Laboratory (630) 252-0529 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] IMCA-CAT Announcement
Dear Colleagues, The IMCA-CAT beamline at the Advanced Photon Source (APS) is continuing to operate and collect crystallography data during the current restricted-access operations at Argonne National Laboratory. Experiments are limited to (1) critical research related to COVID-19 or (2) critical proprietary research related to drug development. All pharmaceutical companies and research entities conducting either COVID-19 related research or critical research in drug discovery are invited to inquire about access to IMCA-CAT for beam time. All experiments must be either remote access or mail-in. IMCA-CAT is committed to accelerating drug discovery through synchrotron-based structural biology research. The insertion device beamline is optimized for delivering exceptional quality data, collecting data at high-throughput rates, and ensuring data security for proprietary experiments. Streamlined pathways for establishing proprietary agreements have been implemented for new industrial users to begin conducting experiments without delay. For more information about accessing IMCA-CAT, please contact Dr. Lisa Keefe (email is keefe [at] imca-cat.org). Work safely and stay healthy, Lisa Keefe - Lisa J Keefe, PhD Director IMCA-CAT Industrial Macromolecular Crystallography Association - Collaborative Access Team 630.252.0544 • Sector 17 @ Advanced Photon Source, Argonne National Laboratory Vice President for Advancing Therapeutics Hauptman-Woodward Medical Research Institute Interim CEO American Crystallographic Association - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] No diffraction
This might be obvious, but make sure you washed the crystals thoroughly before dissolving them for SDS-PAGE or mass spec -Jesse On Thu, Jan 26, 2012 at 10:48 AM, Katherine Sippel katherine.sip...@gmail.com wrote: Might I suggest consulting the CCP4 user community wiki on the topic: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality Good luck, Katherine On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu theresah...@live.com wrote: Dear crystallographers I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa
Re: [ccp4bb] Problem running BALBES
Thank you Fei for your input. Your response inspired me and I found the error I was making (a poorly truncated PDB file). However I have another question regarding BALBES for the brains out there. As I mentioned before, I have a two protein complex with a nice homology model for Protein 1 and the structure of Protein 2 is known (we're using only one domain of Protein 2 in our complex). Balbes finds a solution using the homology model of Protein 1 as an input (Rfree ~ .40) , but it stops there. I was under the impression that the program would then go ahead and try to fit Protein 2 using this newly found solution. It doesn't find a solution when using just the known structure of Protein 2 as a model. Is there a way to accomplish this? Sincerely, Jesse On Wed, Jan 28, 2009 at 1:25 PM, Dr. F Long f...@ysbl.york.ac.uk wrote: Dear Jesse, In both cases, there are some log files under, e,g. Test/process_details/ If you can make tar.gz files on these log files and send them to us. We can analyse what happened in your processes. Thanks, Fei Dr Fei Long Structural Biology Laboratory University of York Heslington York YO10 5YW UK
[ccp4bb] Problem running BALBES
Hello All, I'm trying to use BALBES locally to perform molecular replacement on data of a two protein complex. Protein 1 is a truncated version of a two domain protein of known structure. Protein 2 has a homologous protein of known structure and ~50% identity. I'm having two related problems - 1 If I include the truncated PDB of Protein 1 as an input model, along with a .seq file containing the two sequences, I get the following error: #---# # Search for Structures with Similar Cell and Space Group # #---# No structure of similar cell and space group was found #---# # Model Database Analysis # #---# number of amino acids in the input sequence file is 615 1 structures found to be above 20% identity with the given sequence, of which the best identity is 100.0 Error message : no structure was found ** | All of search model PDB files are in:| |Subdirectory: template_models | ** BALBES exits after searching the internal database 2 If I repeat this, but use a .seq file that has the two sequences merged as one, I get this error: #---# # Search for Structures with Similar Cell and Space Group # #---# No structure of similar cell and space group was found #---# # Model Database Analysis # #---# number of amino acids in the input sequence file is 615 2 structures found to be above 20% identity with the given sequence, of which the best identity is 100.0 can not create a reader object for XML file for /Users/B/Test/xml/get_structure_DB_Protein1.xml Traceback (most recent call last): File /apps/ccp4-6.1.0/bin/balbes, line 154, in module sfAnalysisIni.Sfcheck.info_strucFactor.get_b_overall()) File /apps/BALBES_0.0.1/bin_py/exeCodeClasses.py, line 532, in execute self.SearchDB.controller() File /apps/BALBES_0.0.1/bin_py/exeCodeClasses.py, line 1378, in controller self.structDB_info_analysis() File /apps/BALBES_0.0.1/bin_py/exeCodeClasses.py, line 881, in structDB_info_analysis rootElement = StripXml(struct_xml_document.documentElement) UnboundLocalError: local variable 'struct_xml_document' referenced before assignment Ideas? Any help would be greatly appreciated -Jesse
Re: [ccp4bb] summary: crystals from skin
Are the crystals growing as a result of the skin, or coincidentally located with the skin? For instance, if you are using the hanging drop method, and the crystals are growing with the skin because of their density, you could switch to sitting drop plates -- crystals grow on the bottom, skin stays on top. If the skin is required for crystal growth, then of course this doesn't apply. Generally, this is also simpler than converting the growth conditions from VD to batch under oil. -Jesse On Tue, Dec 30, 2008 at 11:22 AM, riya doreen driy...@gmail.com wrote: Hello Everyone, Thank you for all the suggestions on how to manipulate skin on crystal drops. Here is a summary of responses: (i) Higher concentrations of reducing agents (ii) Layering crystal drop with cryo-protectant (iii) Trypsinize the skin (iv) Grow crystals under oil (v) Try 4C if crystals are grown at 18 or RT (vi) Lower protein concentration and (vii) Fiddling around with the drop which may break the skin and free the crystals On Sun, Dec 28, 2008 at 8:24 PM, riya doreen driy...@gmail.com wrote: *Hello All, I am trying to optimize protein crystals that grow from skin. All efforts to separate crystals from skin have failed since it is fairly thick. Crystallization under oil eliminates skin but the resultant crystals are very thin and small needles. I would appreciate any suggestions on how this problem can be eliminated. Thanks *
Re: [ccp4bb] any review on protein-protein complex crystallization?
This may be obvious, but I would run a size-exclusion column on the complex first. This will give you an idea as to how well these two proteins stick together. On Wed, May 14, 2008 at 4:34 AM, Maarten Dewilde [EMAIL PROTECTED] wrote: Dear CCP4bb, Can anyone point me to good reviews or books which describe how to crystallize protein-protein complexes (or anyone willing to share his/her experience)? In particular I'm interested in: (1) which tests to perform on your complex before you even start thinking about crystallization (2) what should you take in account when you start to crystallize (any other than 'use the Radaev and Sun' screen) (3) how to increase the success rate of crystallization (cross linking? co-expression?) (4) any alternative techniques when crystallization fails (any other than NMR) I would be very grateful! Thanks in advance, Maarten __ Maarten Dewilde - PhD student Laboratory for Pharmaceutical Biology ON2 - PB 824 - Herestraat 49 3000 Leuven [EMAIL PROTECTED] tel: +32 16 323434 fax: +32 16 323460 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.
