Re: [ccp4bb] Intergrown crystals

d try centering on different areas of the crystal to identify a singel crystal. Otherwise, other suggestions of slowing growth rate and micro-seeding should help with your inter-growth problem. Hope this helps, *** Kelly Daughtry, Ph.D. IRTA F

Re: [ccp4bb] Measuring protein concentration with 2mM ATP around

Try preparing your Bradford standard curve with your protein buffer (including the ATP). This is how I reliably get around detergent and other compounds that interfere. Hope this helps, Kelly *** Kelly Daughtry, Ph.D. IRTA Fellow Mechanisms of

Re: [ccp4bb] Microseeding technique advice

treak). Hope this helps, Kelly Daughtry <http://walk.avonfoundation.org/site/TR?px=7043512&pg=personal&fr_id=2260&s_src=BF_emailbadge> *** Kelly Daughtry, Ph.D. IRTA Fellow Mechanisms of Mutation Group Molecular Genetics Labora

Re: [ccp4bb] Resuspension of bacterial cell pellets

vary depending on the media used (i.e. auto-induction media will produce increased cell density), as well as the protein expressed (i.e. toxicity of the target protein leading to cell death and decreased density in the culture). Kelly Daughtry

Re: [ccp4bb] Improvement in crystal quality

edle clusters with a few 0.1 pH unit changes) Dioxane to limit crystal nucleation, try to only add it to the well, not mother liquor present in drop, 1 - 5 % Dioxane Different MW PEGs There are almost limitless possibilities of things to try with protein crystallography. Good luck, K

Re: [ccp4bb] Disulphide bonds and closed conformation

Jan, If the Cys residues are accessible, you could try DTNB to quantify the number of Cys, thus determining if they are reduced or bridged. http://en.wikipedia.org/wiki/Ellman's_reagent Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral F

Re: [ccp4bb] FE-Sulfur proteins

*should* work with other FeS containing enzymes. Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178

Re: [ccp4bb] FE-Sulfur proteins

Jan, Do you express the protein with the *E. coli isc* iron-sulfur cluster synthetic operon? I found great success, see: Daughtry, KD et. al. JACS 2012 http://pubs.acs.org/doi/full/10.1021/ja2111898 - Kelly Daughtry *** Kelly Daughtry, Ph.D

Re: [ccp4bb] Expressed protein hinders cell lysis?

If it is inclusion bodies, I generally see a milky solution after lysis. Have you centrifuged post-lysis and then run an SDS-PAGE? Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H

Re: [ccp4bb] Strange Density

*** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *** On Tue, May 15, 2012 at 10:51 AM, RHYS

Re: [ccp4bb] Anaerobic glovebox crystal cryo-cooling

ation when heading into LN2 (i.e.increased time spent hovering over LN2 in the gas/semi cool area) can cause ice. Thus I always try to plunge in quickly, then maneuver to the desired storage location (puck, cap). Kelly ******* Kelly Daughtry, Ph.D. Pos

Re: [ccp4bb] dea all

you try other tags (GST, MBP, etc)? Hope this helps, Kelly Daughtry *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-

Re: [ccp4bb] DDM

*** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *** On Mon, Mar 26, 2012 at 1:17 PM, Katarzyna Rudzka wrote: >

Re: [ccp4bb] Temp Fact Variance Analysis

specific side chains compared to main chain atoms. Hope this helps clarify. Sincerely, Kelly Daughtry *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research

Re: [ccp4bb] HKL2000 indexing problem

ry to process my data in several programs in parallel. Best, Kelly Daughtry *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P

Re: [ccp4bb] surface residue mutation

SC, Kent SB. http://www.ncbi.nlm.nih.gov/pubmed/1604320 Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684

Re: [ccp4bb] To archive or not to archive, that's the question!

as they like. I would happily upload a few data sets. (Just a suggestion) Best Wishes, Kelly Daughtry *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

schedule appointments much sooner than GE as well. It could be useful to see if such a company is located near you. Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303

Re: [ccp4bb] Difficulty indexing diffraction, cell too small

people just use XDS and assume everything went well, and run into similar problems. Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Dur

Re: [ccp4bb] mtz2various command line R-free label?

to ensure I have my original test set carried over and do it simply from the command line. The program works perfectly fine within the CCP4 GUI. If no command line option is found, that is ok. I just want to ask everyone to see if it was do-able. Thanks again! Kelly Daughtry

[ccp4bb] mtz2various command line R-free label?

x27;t always have to open the GUI for one task). Thanks in advance for any help you can provide! Kelly Daughtry *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Res

Re: [ccp4bb] pdb formats

Notepad++ is a free windows text editor that recognizes the line breaks, and does a multitude of other functions. http://notepad-plus-plus.org/ <http://notepad-plus-plus.org/>Best, Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow,

Re: [ccp4bb] thread protein sequence using pdb coordinates that are not avaliable on RCSB?

Thanks for all the suggestions. I was able to use swiss-pdb viewer to accomplish my goal within 2 minutes of installing! Very useful software in general! I didn't realize all of the tools present. Thank you everyone! Kelly *** Kelly Dau

[ccp4bb] thread protein sequence using pdb coordinates that are not avaliable on RCSB?

to select a PDB ID, and not to upload your own pdb file. Does anyone know where I can do this online? I'm thisclose to just changing each amino acid in coot (with the amount of searching I've done, it's about equal time!). Thanks in advance,

Re: [ccp4bb] problem with residue numbering and Coot

refinement's easier) if you follow the actual numbering within your protein. Just my two cents. Any other suggestions about standard numbering nomenclature? Kelly Daughtry ******* Kelly Daughtry PhD Candidate Department of Physiology and

Re: [ccp4bb] An alternative to glycerol in keeping protein soluble?

would suggest stepping down the glycerol concentration gradually while increasing the precipitant. Good luck, Kelly *** Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth

Re: [ccp4bb] Crystal rescue

. Kelly *** Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *** On Tue

Re: [ccp4bb] Acidic protein purification

e detailed information about pH stability of each resin type as well. Kelly ******* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 61

Re: [ccp4bb] smeared spot in diffraction

diffusion to give better ordered crystals). Kelly Daughtry *** Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548

[ccp4bb] ligand with alternate conformation?

file, but that is not correct as the CIF file thinks that they are both fully there (i.e. no occupancy in the CIF file) (used phenix.elbow to generate CIF files). Any suggestions on how to move forward? Thanks in advance, Kelly ******* Kelly Da