Re: [ccp4bb] Intergrown crystals

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 Fellow

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

Re: [ccp4bb] Microseeding technique advice

). Hope this helps, Kelly Daughtry http://walk.avonfoundation.org/site/TR?px=7043512pg=personalfr_id=2260s_src=BF_emailbadge *** Kelly Daughtry, Ph.D. IRTA Fellow Mechanisms of Mutation Group Molecular Genetics Laboratory, MD E-301 National

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

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, Kelly Daughtry

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] FE-Sulfur proteins

it *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] 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 Fellow

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] dea all

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: 919-684-5178

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 kasiarud

Re: [ccp4bb] Temp Fact Variance Analysis

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 Drive RM 250 Durham, NC

Re: [ccp4bb] HKL2000 indexing problem

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: 919

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

, they 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

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 Durham, NC 27710 P

[ccp4bb] mtz2various command line R-free label?

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 Research

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

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 Daughtry

Re: [ccp4bb] problem with residue numbering and Coot

) 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 Biophysics Boston University

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

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) 617-358-5548

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?

, 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 Daughtry PhD