Re: [ccp4bb] MALLS analysis question

very large things will have a scattering profile that doesn't align well at all with the UV and RI. What I usually do is use the alignment parameters from a small, more isotropic scatterer like cytochrome C or RNase A at high concentration for my experimental runs. Hope this helps, Kushol

Re: [ccp4bb] 250 kDa standard

The Catalase tetramer is around there (232 kD according to the Table 1 in Mylonas and Svergun, J. Applied Cryst. 2007). The shape of the tetramer in the PDB (4BLC) seems reasonably globular. Cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of

Re: [ccp4bb] DNA oligonucleotide purification

0/l p-73370.html http://www.dionex.com/en-us/products/columns/bio/nucleic-acid/dnapac-pa200/l p-73371.html cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine mailto:kgu...@stwing.upenn.edu> kgu...@mail.med.u

Re: [ccp4bb] DNA oligonucleotide purification

We're using an older Dynamax system that is outfitted with PEEK throughout. Cheers, Kushol From: Wallen, Jamie [mailto:jwal...@biochem.wustl.edu] Sent: Thursday, April 28, 2011 10:17 AM To: Kushol Gupta; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] DNA oligonucleotide purific

Re: [ccp4bb] {**SPAM**} [ccp4bb] screen kit

, Issues 1-4, November 2001, Pages 409-417 Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On

Re: [ccp4bb] Histogram/Plot of Buried Surface Areas

computed hydrodynamic properties to those observed in gel filtration or centrifugation or SAXS or the like) could help flesh out these types of questions. Hope this helps, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine kgu

Re: [ccp4bb] larger molecular weight shown by analytic ultracentrifugation

sedimentation velocity. Hope this helps, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine mailto:kgu...@stwing.upenn.edu> kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 From: CCP4 bulletin board [mailto:CCP

Re: [ccp4bb] larger molecular weight shown by analytic ultracentrifugation

mass. Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine mailto:kgu...@stwing.upenn.edu> kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 From: Chad Brautigam [mailto:cabrautc...@yahoo.com] Sent: Thursday, J

Re: [ccp4bb] LS / RI detector systems

ood, too. Hope this helps, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tommi K

Re: [ccp4bb] Postdoc wanted - NIST-ARRA Fellowship Program

Please respond to Joseph Curtis (joseph.cur...@nist.gov) and Susan Krueger (susan.krue...@nist.gov ) if you are interested. =-=- Here is the link. NIST-ARRA Fellowship Program http://www.nistfellows.umd.edu/index.htm If there is someone that is interested then they should contact

Re: [ccp4bb] SAXS on a coiled coil protein

ery active community of small-angle scattering geeks on the forum at www.saxier.org - might be worth posting this question there as well. Cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine mailto:kgu...@stwing.upen

Re: [ccp4bb] SAXS EM comparison

, but that might be worth googling as well. Cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 Dear all, the other day I obtained SAXS data from which a low-resol

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

sounds like you have other data - do the theoretical Rs, f/fo, etc of the shapes generated agree well with your other measurements? Cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine kgu...@mail.med.upenn.edu 215-573-7260

Re: [ccp4bb] monomer-dimer

Hi Maia, this review and website might be a good place to start: http://analyticalultracentrifugation.com/images/AUCinProteinScience.pdf http://analyticalultracentrifugation.com/default.htm Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School

Re: [ccp4bb] small-angle scattering and radiation damage control

Does the beamline have an attenuator? (I'm pretty sure SSRL BL4-2 has a series of them that can be flipped on.) cheers, Kushol Kushol Gupta, Ph.D. Mathilde Krim Fellow in Basic Biomedical Research Van Duyne Laboratory - Univ. of Pennsylvania School of Medicine kgu...@mail.med.upenn.edu 21

Re: [ccp4bb] tips on crystallizing a Protein-DNA complex

, Crystallization of bFGF-DNA aptamer complexes using a Sparse Matrix designed for protein–nucleic acid complexes Journal of Crystal Growth, 2001 232 (2001) 409–417 cheers, Kushol Kushol Gupta, Ph.D. Mathilde Krim Fellow in Basic Biomedical Research Van Duyne Laboratory - Univ. of

Re: [ccp4bb] Puzzling observation about size exclusion chromatography

Isn't 18 mLs into a Superdex 200 10/300 column run out near where the 670kD marker is, just after the void at ~15 mLs? Zhen, did you mean ~500kD rather than 5kD?. Kushol Kushol Gupta, Ph.D. Research Associate - Van Duyne Laboratory Perelman School of Medicine University of Pennsyl

Re: [ccp4bb] Puzzling observation about size exclusion chromatography

Mea culpa - I'm thinking minutes at 0.5 ml/min, not mLs! (clearly I'm overdue for my afternoon caffeine...) Kushol -Original Message- From: Zhang, Zhen [mailto:zhen_zh...@dfci.harvard.edu] Sent: Thursday, June 20, 2013 4:18 PM To: 'Kushol Gupta'; CCP4BB@JISCMA

Re: [ccp4bb] Problems with SANS data analysis

ed for reduction. HTH, Kushol Kushol Gupta, Ph.D. Research Associate - Van Duyne Laboratory Perelman School of Medicine University of Pennsylvania mailto:kgu...@stwing.upenn.edu> kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 From: CCP4 bulletin board [mailto:CCP4BB@JIS

Re: [ccp4bb] SAXS facility and Cryo EM facility

What part of the world are you in? Kushol Kushol Gupta, Ph.D. Research Associate - Van Duyne Group Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:kgu...@upenn.edu> kgu...@upenn.edu / 215.573.7260 / 267.25

[ccp4bb] Register Now! ACA 2018 - Small Angle Scattering Workshop

Lunch will be included. Contact: Kushol Gupta, Perelman School of Medicine, University of Pennsylvania. <mailto:kgu...@upenn.edu> kgu...@upenn.edu Confirmed Instructors: Angela Criswell, Rigaku Corporation Srinivas Chakravarthy, BioCAT Group, Advanced Photon Source Richard Gillilan, Ma

Re: [ccp4bb] SEC and MALS

mmonly misunderstood). Kushol Kushol Gupta, Ph.D. Research Assistant Professor, <https://www.med.upenn.edu/biocbiop/index.html> Department of Biochemistry and Biophysics Director, <https://www.med.upenn.edu/jf/bsbcore/index.html> Johnson Foundation Structural Biology and Bioph

[ccp4bb] FW: post-doc opening at NCNR/NIST

Hi all, See below and contact Joseph Curtis (joseph.cur...@nist.gov) for more information. Kushol Kushol Gupta, Ph.D. Research Associate - Van Duyne Group Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:

Re: [ccp4bb] asymmetric homotrimer in the asu

your SAXS expt, start at a sample concentration where MW (kD) * concentration (mg/mL) ~100 and then adjust accordingly. (I’ve successfully studied molecules as small as a 8.5 kD Tudor domain and a ~7kD CHAPS micelle in this way.) Hope that helps, Kushol Kushol Gupta, Ph.D

[ccp4bb] Federal Post‐Doctoral Fellowship Opening: Joint project between MedImmune & NIST

dson (steven.hud...@nist.gov). Kushol Gupta, Ph.D. Research Associate - Van Duyne Group Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:kgu...@upenn.edu> kgu...@upenn.edu / 215.573.7260 / 267.259.0082 / <http://www

Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope

correlation coefficient for fits. Hope that helps, Kushol Kushol Gupta, Ph.D. Research Associate - Van Duyne Group Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:kgu...@upenn.edu> kgu...@upenn.edu / 215.57

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

is would be to start with CRYSOL and see what the discrepancy between the structure and the primary scattering and in what part of the data those discrepancies lie. I can suggest a number of citations on each of the bullet points above if you'd like. Good Luck, Kushol Kushol Gupta, P

Re: [ccp4bb] R: [ccp4bb] fit multiple structures into SAXS envelope

aren’t the same thing as EM reconstructions, and can be horribly misleading if parts of your atomic inventory are flexible or disordered. (what are your NSD values for the bead calculations using what program? What do your Kratky and Porod-Debye plots look like?) Kushol Kushol Gupta

Re: [ccp4bb] Do my SAXS data agree with the crystal structure?

crepancies like those you note should be expected. Hope that helps, Kushol Kushol Gupta, Ph.D. Research Associate - Van Duyne Laboratory HHMI / Perelman School of Medicine University of Pennsylvania kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 -Origin

[ccp4bb] ACA 2018 - Small Angle Scattering Workshop

is mandatory. The fee to attend is: * Student (undergrad, grad or postdoctoral) - $185 (CAN) * Corporate - $355 (CAN) * Non-corporate or non-student - $185 (CAN) Lunch will be included. Contact: Kushol Gupta, Perelman School of Medicine, University of Pennsylvania. <