[ccp4bb] Cysteine sulfenic acid in coot

odelling > Replace Residue"...option to change it. Thanks in advance for your suggestions and happy holidays! Best regards, Sudipta -- Sudipta Bhattacharyya, PhD Assistant Professor, Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur,

Re: [ccp4bb] Protein is dimmer in solution, hard to build two chains in crystal structure

Hello Zhou, How sure are you about the space group of the solution? Any signs of twinning or t-NCS? Best, Sudipta. On Mon, Aug 20, 2018, 7:36 PM SUBSCRIBE CCP4BB Zhu Qiao < jasonqia...@gmail.com> wrote: > Hi All > > My protein is dimer both in protein buffer and crystallisation reservoir, > whi

Re: [ccp4bb] pseudo-centering or twinning problem in P3

worked for me. Cheers, Sudipta. Sudipta Bhattacharyya, Postdoctoral fellow Department of Molecular Biosciences University of Texas at Austin Texas, USA. On Tue, Aug 8, 2017 at 8:27 AM, Eleanor Dodson wrote: > First of all - check whether your crystal data shows twinning - thee is an >

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

Hi Rhys, Along with what others have suggested, you can always try prosmart refinement. I found it really helpful in my cases. Best of luck, Sudipta. Sudipta Bhattacharyya Postdoctoral research fellow University of Texas at Austin Texas, USA. On Jul 12, 2017 6:20 PM, "Rhys Grinter&qu

Re: [ccp4bb] Substrate density visible in relatively active mutant

condition compared to the wild type version. Best, Sudipta. Sudipta Bhattacharyya Postdoctoral fellow, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA. On Fri, May 26, 2017 at 3:48 PM, Seema H Irani wrote: > I crystallized a PLP dependent enzyme and wanted

Re: [ccp4bb] No improvement in R-factor after Refmac.

Hi Satya Dev, You can feed the mtz output of SCALA to Phenix Xtriage and then see the presence of t-NCS and/or any other crystal pathologies. Another thing you can do is to merge and scale the data in P222 and then let the Phaser decide the best space group. Again, I am curious, when you ran point

Re: [ccp4bb] Problem with MolRep

Dear Madhurima, More information is needed regarding data processing/scaling, initial space group, NCS etc...Then the community can help you better. Anyway, I hope the crystal you got and collected the data are your target protein's...How sure you are you? How purified your sample is? Did you diss

Re: [ccp4bb] R/Rfree values

Hi Rohit, Along with many excellent suggestions you already got...I want to add the possibility of the presence of twining (even a small but significant percent) and/or the presence of t-NCS in the data. Good luck! Sudipta. On Wed, Dec 14, 2016 at 12:19 PM, Prem Prakash wrote: > Dear Rohit, >

Re: [ccp4bb] Twinning/Spacegroup Woes

Hi Rhys, We had a similar problem where initial data processing suggested P6522 space group but the content of the crystal was too large to fit in the unit cell (one well known symptom for twining). I reprocessed the data in P6, P312, P321 and finally the solution was obtained in P6 (P65). Howeve

Re: [ccp4bb] Ambiguous metal ion at active site.

Hi Dilip, More information is needed regarding the crystallization condition(s). Anyway, Mg2+ ions are always (most of the time) are surrounded by water molecules in their primary hydration sphere...(typical distance should be 2.2 A, if I remember correctly)...and the typical geometry would be oct

Re: [ccp4bb] Picking water molecules at 4A structure.

Dear all, I thank you all for your kind suggestions and remarks. So the bottom line appeared to me is - one should not pick water molecules at low resolution (grater than 3.0/3.5A) data (not a truncated data I guess) unless there is sufficient reasons/evidences (like presence of water molecules at

[ccp4bb] Picking water molecules at 4A structure.

Dear community, Recently we have been able to solve a crystal structure of a DNA/protein complex at 4A resolution. After almost the final cycles of model building and refinement (with R/Rfree of ~ 22/27) we could see some small water like densities...all throughout the complex. Now my query is, wh

[ccp4bb] Can nucleoprotein complex inhibit EtBr binding?

Dear Community, Sorry for this off topic question. I am dealing with a non specific DNA binding protein. In a non radio-labelled EMSA DNA:protein titration experiment when I EtBr stained the 5% native acrylamide gel, I could see the DNA control (101 bps) but as the amount of my protein increases I

[ccp4bb] Problem regarding twin detection and refinement

4A resolution could anyone tell me what final R/Rfree one could expect from a 4A data (although it may sound a dumb question...) Any help will be highly appreciated. With my best regards, Sudipta. Sudipta Bhattacharyya, Postdoctoral Research Fellow, Colorado State University, Fort Collins

Re: [ccp4bb] Translational NCS and molecular replacement.

. If you use the same a, b and c >> axes as before, you do not need to rerun Phaser, otherwise you have to. >> >> If you have translational NCS, you have to live with it. The only way to >> get rid of it is to find another crystal with a different crystal packing. >> >>

[ccp4bb] Translational NCS and molecular replacement.

Dear Community, I have some doubts to clarify. In a way to solve a structure by Phaser-MR, I found phaser ended up with a potentially good MR solution (with good statistics, packing and electron density, and as we know the homolog structure so in a reasonable biological assembly also). However, th

[ccp4bb] homology modeling of dimeric proteins

is fine!!! Please suggest something that would be fruitful. Thanking you in advance for your kind cooperation. Regards, Sudipta Bhattacharyya, Department of Biochemistry and Molecular Biology, Colorado State University.

Re: [ccp4bb] Fitting of a trigonal bipyrimidal phosphorus

Dear all, Thanks for your cooperation. Regards, Sudipta. Sudipta Bhattacharyya, Senior Research Fellow, Department of Biotechnology, Indian Institute of Technology Kharagpur, India. > >

[ccp4bb] Fitting of a trigonal bipyrimidal phosphorus

Dear all, Could anybody please tell me how to get the coordinate file and the cif file for the trigonal bipyramidal (TBP) phosphorus (figure given below for your convenience)? Prodrg server is not helping out in this issue. Thanks in advance. Regards, Sudipta. Sudipta Bhattacharyya Senior

Re: [ccp4bb] Off topic: Request for a soft copy of a book

Dear all, Thank you for your help and suggestions. Actually I need to consult the book in order to analyze some of our experimental results and I was in a bit hurry. Honestly my intention was not however, to violate the copyright issues but I thought scientific problems demands much than the mere

Re: [ccp4bb] NADP binding protein without Rossmann fold.

Dear all, Thank you very much for your cooperation. Regards, Sudipta. Sudipta Bhattacharyya. Senior Research Fellow, Department of Biotechnology, Indian Institute of Technology Kharagpur, India.

[ccp4bb] NADP binding protein without Rossmann fold.

please cite or suggest any other example of such type of anomaly? Is there any example of non-classical Rossmann fold bearing proteins? Thanks, Sudipta. Sudipta Bhattacharyya. Senior Research Fellow, Department of Biotechnology, Indian Institute of Technology Kharagpur, India.