[ccp4bb] RMSD of dimers
I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan
[ccp4bb] error message in xds
Dear All, I am getting an error message after indexing the data in XDS as !!! ERROR !!! DIMENSION OF DIFFERENCE VECTOR SET 2 , please suggest what wrong has happened and what could be done for this, initially the message was insufficient number of spots accepted was there, then I change the resolution range from 20 3.5 to 20 0 0 0, then I got the above mentioned error. Thank you in advance. Jeorge
Re: [ccp4bb] error message in xds
Hi, As I understand it you don't have enough spots for indexing. You may want to try and increase the number of frames from which spots are taken for indexing (SPOT_RANGE), maybe even to the maximum. You can have a look at COLSPOT.LP (the printed output of the spot collecting process) and SPOTS.XDS (where spots coordinates are stored). Other things to check would be the origin coordinates. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jeorgemarley thomas [kirtswab...@gmail.com] Sent: Tuesday, February 24, 2015 9:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] error message in xds Dear All, I am getting an error message after indexing the data in XDS as !!! ERROR !!! DIMENSION OF DIFFERENCE VECTOR SET 2 , please suggest what wrong has happened and what could be done for this, initially the message was insufficient number of spots accepted was there, then I change the resolution range from 20 3.5 to 20 0 0 0, then I got the above mentioned error. Thank you in advance. Jeorge
[ccp4bb] Postdoc in Membrane Protein Structural Biology
POSTDOCTORAL POSITION IN MEMBRANE PROTEIN STRUCTURAL BIOLOGY A NIH funded postdoctoral position is available immediately in the laboratory of Dr. Francis Valiyaveetil, Department of Physiology and Pharmacology, Oregon Health and Science University in Portland, Oregon. The Valiyaveetil group investigates the structure and function of ion channels and transporters using a combination of unnatural amino acid mutagenesis, electrophysiology and x-ray crystallography. See references (Proc. Natl. Acad. Sci. 110, 17886, 2013; Proc. Natl. Acad. Sci. 110, 15698, 2013) for an example of the research underway in the lab. The position is suitable for a highly motivated candidate with a recent (less than 1 year) Ph.D. in biochemistry, biophysics or a related discipline who has gained extensive experience in protein crystallography in their graduate research. The position provides the candidate with a unique opportunity to gain expertise in membrane protein biochemistry, electrophysiology and techniques for unnatural amino acid mutagenesis. Please send CV, a brief description of graduate research, future research interests and contact information for three references by email to: valiy...@ohsu.edu OHSU is an equal opportunity, affirmative action institution. Dr. Francis I. Valiyaveetil Assistant Professor Program in Chemical Biology Department of Physiology and Pharmacology Oregon Health and Science University 3181 SW Sam Jackson Park Road Portland, OR USA 97239-3098 email: valiy...@ohsu.edu
[ccp4bb] collection strategy to collect the intersection with a reference set.
Hi all, I'm on the lookout for a prediction program that'll tell me the best collection angles that match the reflections of a reference set, as opposed to the the reflections that'll complete a reference set. It seems that mosflm and XDS prescribe the angles for completion rather than the intersection. Thanks, F
[ccp4bb] Postdoctoral position
Please could you advertise the attached postdoc position? BBSRC-postdoc.doc Description: application/applefile BBSRC-postdoc.doc Description: Binary data Dr. Belinda BullardDept. of BiologyUniversity of YorkYork YO10 5DDUKTel 44(0)1904 328823FAX: 44(0)1904 328825email:bb...@york.ac.uk
Re: [ccp4bb] collection strategy to collect the intersection with a reference set.
Hi Francis, XDS (XPLAN) just prints tables. Instead of looking in these for the range that maximizes the total completeness, you could just minimize the total completeness. This would maximize the intersection. HTH, Kay On Tue, 24 Feb 2015 11:37:05 -0500, Francis Reyes francis.re...@colorado.edu wrote: Hi all, I'm on the lookout for a prediction program that'll tell me the best collection angles that match the reflections of a reference set, as opposed to the the reflections that'll complete a reference set. It seems that mosflm and XDS prescribe the angles for completion rather than the intersection. Thanks, F
Re: [ccp4bb] RMSD of dimers
Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!). See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote: I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
[ccp4bb] Postdoc position in structural biology of multiprotein complexes, SGC University of Oxford
Dear all, We seek a post-doctoral scientist with strong background in structural biology and protein-protein interactions, to drive an industry-funded project studying the molecular mechanism of iron-sulphur cluster assembly and associated genetic disorders. http://www.ndm.ox.ac.uk/current-job-vacancies/vacancy/117257-Postdoctoral-Research-Scientist-Structural-Biology-in-Rare-Diseases Closing date: Monday 16th March 2015, 12pm GMT Visit the SGC Metabolic Rare Diseases group page: http://www.thesgc.org/science/mob Informal enquiries to: wyatt@sgc.ox.ac.uk - Dr Wyatt W. Yue Principal Investigator, Metabolic Rare Diseases Structural Genomics Consortium University of Oxford UK OX3 7DQ +44 (0)1865 617757 http://www.thesgc.org/wyatt
[ccp4bb] Post-doctoral position
University of York, Department of Biology Post-doctoral Research Associate The molecular basis of stretch activation in muscle A post-doctoral position is available to work on the stretch activation of muscle, using insect flight muscle (Lethocerus and Drosophila) as a model system. The aim of the project is to find out how the regulatory complex, troponin, senses stretch. The structure of the complex and the interaction of subunits within the complex will be investigated, as well changes in the structure occurring when the muscle is stretched. The project will involve, molecular biology, protein chemistry and spectroscopic techniques. The position is funded by the BBSRC for 3 years and is available from April 1 2015. The starting salary is £30,434 – £31,342 per annum. Enquiries can be made to belinda.bull...@york.ac.uk. The closing date is March 12 2015. Dr. Belinda Bullard Dept. of Biology University of York York YO10 5DD UK Tel 44(0)1904 328823 FAX: 44(0)1904 328825 email: bb...@york.ac.uk
Re: [ccp4bb] hydrophilic protein going to aggregate
Hi Anita, Try to lower the ph of binding buffer if your protein allows also you may lower the concentration of salt like nacl if adding into the buffer also try to reduce the imidazole concentration of your eluted fraction gradually by performing serial dialysis before SEC. Alternatively, you can try cobalt IMAC instead of nickel which may have lower affinty to proteins his tag. Also it may possible that your trucated construct may have lesser stability. You can also try to add some additives like glycerol to improve its stability along with some reducing agent like DTT or TCEP. Hope this may help your protein. Shivendra On Feb 25, 2015 9:13 AM, Anita P crystals...@gmail.com wrote: Hello Crystallographers, I am trying to express and purify a soluble domain of a membrane protein for crystallization. The amino acid content is as below Ala (A) 12 13.8% Arg (R) 10 11.5% Asn (N) 2 2.3% Asp (D) 8 9.2% Cys (C) 1 1.1% Gln (Q) 1 1.1% Glu (E) 4 4.6% Gly (G) 16 18.4% His (H) 3 3.4% Ile (I) 0 0.0% Leu (L) 3 3.4% Lys (K) 1 1.1% Met (M) 1 1.1% Phe (F) 2 2.3% Pro (P) 6 6.9% Ser (S) 11 12.6% Thr (T) 1 1.1% Trp (W) 1 1.1% Tyr (Y) 1 1.1% Val (V) 3 3.4% I could purify the protein using IMAC to 95% purity, how ever, I had to elute with very high concentration of imidazole 2 M, still some protein is attached to the beads as I could observe on the SDS PAGE. I concentrated the protein to 25 mg/ml of 3 mls and on performing SEC, I found the protein to be in the Void fraction of SEC 200. Any expert advice on how to optimize this purfication and why it is still attached to the beads? thanks in advance Anita
[ccp4bb] hydrophilic protein going to aggregate
Hello Crystallographers, I am trying to express and purify a soluble domain of a membrane protein for crystallization. The amino acid content is as below Ala (A) 12 13.8% Arg (R) 10 11.5% Asn (N) 2 2.3% Asp (D) 8 9.2% Cys (C) 1 1.1% Gln (Q) 1 1.1% Glu (E) 4 4.6% Gly (G) 16 18.4% His (H) 3 3.4% Ile (I) 0 0.0% Leu (L) 3 3.4% Lys (K) 1 1.1% Met (M) 1 1.1% Phe (F) 2 2.3% Pro (P) 6 6.9% Ser (S) 11 12.6% Thr (T) 1 1.1% Trp (W) 1 1.1% Tyr (Y) 1 1.1% Val (V) 3 3.4% I could purify the protein using IMAC to 95% purity, how ever, I had to elute with very high concentration of imidazole 2 M, still some protein is attached to the beads as I could observe on the SDS PAGE. I concentrated the protein to 25 mg/ml of 3 mls and on performing SEC, I found the protein to be in the Void fraction of SEC 200. Any expert advice on how to optimize this purfication and why it is still attached to the beads? thanks in advance Anita
