Re: [ccp4bb] Fo-Fc density close to cysteine residue

For some reason if your sulfur on cysteine becomes sulfide anion, you can model sodium/potassium. Distance seems to be optimum for S...Na contact. Since you do not see any anomalous signal, this is one possibility. I also see small blobs around which may resolve to be water molecules. Anthony

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Lumbini, It would useful to know the distance between the sulfur and center of the Fo-Fc map that you have shown. Since you have very high resolution data, the extra density could be for a hydrogen atom in CSO-H (sufeneic acid) or anisotropy of the oxygen atom. Anthony From: 176a9d5eba

Re: [ccp4bb] Live stream of CCP4 Study Weekend?

# > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- Dr. Anthony Addlagatta Principal Scientist Center for Chemical Biology CSIR-Indian Institute of Chemical Technology [IICT] Tarn

Re: [ccp4bb] Crystals Disappearing Overnight

ecomes homogenous that may dissolve the crystals. To rule out this, set up two crystallization experiments under similar conditions. 1) only the protein 2) only the adenosine Regards Anthony - Dr. Anthony Addlagatta Center for Chemical Biology

Re: [ccp4bb] AW: [ccp4bb] protein polymerization

polymerizing. This could be a simple precipitation. Please check your pH, salt conditions or if you require some co-factors etc in addition to checking with bME as suggested by Herman. Anthony - Dr. Anthony Addlagatta Center for Chemical

Re: [ccp4bb] unexplained density

you should know the source). Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home

Re: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex

/WWWrobots/newsletters/Newsletter_july_2011.pdf Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site

Re: [ccp4bb] Backbone hydrogen bonds in protein

. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Mohan Pradhan To: CCP4BB

Re: [ccp4bb] Off Topic- Cystine Detection

- Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message

Re: [ccp4bb] need some suggestions for crystallization

commercial interest with Rigaku. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict

Re: [ccp4bb] electron density assignment

your central atom which makes them all fall in the same plane. From the density it looks more like a water in the center but anomalous density map should help. Good luck. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian

Re: [ccp4bb] how many metal sites

s 111–120 Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlaga

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....

ntical set from the authors. This, not only will give confidence to the "genuine scientist" but will also keep a check on the perpetrators and more responsibility on the reviewers/publishers. Anthony --------- Dr. Anthony Addlagatta

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Nice link. Thanks Anthony - Dr. Anthony Addlagatta

Re: [ccp4bb] improvement of tiny protein crystals

ONATE. Play little bit with pH. Good luck Anthony - Dr. Anthony Addlagatta Scientist E1 Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191583 -- Original Message --- From:

[ccp4bb] Exciting fellowships in India

Sorry for the off topic. DBT New Delhi has announced exiting fellowships for the Scientist of Indian Origin who wish to take up faculty positions in India in the area of Bioenergy. For more details check DBT site at http://dbtindia.nic.in/news_management/PressreleaseDetails.asp?PressId=83&butt

[ccp4bb] Exciting postdoctoral fellowships in India

h weather like southern Texas. Anyone interested in molecular, structural and/or cell biology can send in your inquiries to anth...@iict.res.in or addlaga...@yahoo.com. Anthony - Dr. Anthony Addlagatta Scientist E1 and Ramanujan Fellow C

Re: [ccp4bb] off-topic: Compound search by chemical similarity

1070 Bruxelles, BELGIUM > e-mail: cedric.bauv...@ulb.ac.be > tél: +32 (0)2 5273634 > fax: +32 (0)2 5267273 > ...... - Anthony Addlagatta, Ph.D. Ramanujan Fellow and Sen

Re: [ccp4bb] Offtopic-ish: Ubuntu Laptop

Molecular Biology > Room 10102 New College Building > 245 N. 15th St. > Philadelphia, PA 19102 > > Phone: (+) 215-762-7316 > Fax: (+) 215-762-4452 - Anthony Addlagatta, Ph.D. Ramanujan Fellow and Senior Scientist Center for Chemic

Re: [ccp4bb] removal of dimer

can dialysis help > me. kindly guide me as i have to formulate the product and fill it quickly. > > Thanks in anticipation. > > meg --------- Anthony Addlagatta, Ph.D. Ramanujan Fellow and Senior Scientist Center for Chemical Biology I

Re: [ccp4bb] moving the cofactor in model

9 11:26:35 +, Elad Binshtein wrote > i have a density map and a model and i want to place the cofactor. > i use wincoot and find the electron density for the cofactor but... > how can i move the cofactor and play with it in this area? ---------

Re: [ccp4bb] PEG3350-based cryoprotectant

lecular Pharmacology > 970L Lazare Research Building > University of Massachusetts Medical School > 364 Plantation Street > Worcester, MA 01605 - Anthony Addlagatta, Ph.D. Ramanujan Fellow and Senior Scientist Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad- 57, INDIA Tel:+91-40-27191583 Url: http://www.iictindia.org/zacb/Dr.%20Anthony.aspx

Re: [ccp4bb] Posttranslational modifications of recombinant proteins expressed in E. coli?

> > Any comments will be greatly acknowledged. Thanks a lot in advance, Alfredo. > > Alfredo Torres-Larios, PhD > Assistant Professor > Instituto de Fisiologia Celular, UNAM > Circuito Exterior S/N. Ciudad Universitaria > Mexico, DF, Mexico > >

Re: [ccp4bb] organic Cl as H-bond acceptor?

ake the H-bond. > > Thanks, > Ed --------- Anthony Addlagatta, Ph.D. Ramanujan Fellow and Senior Scientist Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad- 57, INDIA Tel:+91-40-27191583 Url: http://www.iictindia.org/zacb/Dr.%20Anthony.aspx

[ccp4bb]

ates > with > angstroem units? thanks, Katja --------- Anthony Addlagatta, Ph.D. Ramanujan Fellow and Senior Scientist Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad- 57, INDIA Tel:+91-40-27191583 Url

Re: [ccp4bb] protein degradation?

protein with the N- terminal His-tag sticks to the metal affinity resin. So you assume that nothing is wrong with the amino terminus. It is worth looking at this aspect in addition to several other good suggestions. Good luck! Anthony Anthony Addlagatta, PhD

Re: [ccp4bb] Modified N-terminal throenine?

Have you considered it to be a disordered terminus with some waters extending the density (at least in B1 from your figures)? Anthony Anthony Addlagatta, PhD Institute of Molecular Biology University of Oregon Eugene, OR-97403 Phone: (541) 346-5867 Fax: (541

Re: [ccp4bb] The importance of USING our validation tools

give his/her recommendations independent of the actual contents of the manuscript. it could be another independent referee or a hired crystallographer (one more job!!). Anthony Anthony Addlagatta, PhD Institute of Molecular Biology University of Oregon Eugene

Re: [ccp4bb] Volume calculation of a crevice

Try the CASTp site at http://sts.bioengr.uic.edu/castp/calculation.php Anthony Anthony Addlagatta, PhD Institute of Molecular Biology University of Oregon Eugene, OR-97403 Phone: (541) 346-5867 Fax: (541)346-5870 Web: http://uoregon.edu/~anthony On Aug 3

Re: [ccp4bb] stacking interaction!

Server issue):W473-6. Epub 2007 Jun 21. PMID: 17584791 [PubMed - in process] The server can be accessed @ http://crick.mbu.iisc.ernet.in/~PIC Good luck! Anthony Anthony Addlagatta, PhD Institute of Molecular Biology University of Oregon Eugene, OR-97403 Phone

Re: [ccp4bb] density map

Could it be an oxalate? O2C-CO2 Just a guess Anthony Anthony Addlagatta, PhD Institute of Molecular Biology University of Oregon Eugene, OR-97403 Phone: (541) 346-5867 Fax: (541)346-5870 Web: http://uoregon.edu/~anthony On Jul 26, 2007, at 3:10 PM, Wu

Re: [ccp4bb] advice for crystallizing hydrophobic small molecules

really well, at least those I synthesized. People, some times use crystallization techniques similar to protein like hanging or sitting drops for some small molecules, particularly those are water soluble. Good luck Anthony Anthony Addlagatta, PhD Institute

[ccp4bb]

Seeding! AA On Jun 8, 2007, at 9:03 AM, sajid akthar wrote: Hi All I'm getting clusters of crystals (tiny and long needles) and I'm trying to get good single crystals. Even I'm getting the same result at low salt concentrations. I reduced the temperature to slow down the evaporation, st