[ccp4bb] Ligand fitting into density

of the compound is fitting well enough into the density. The B factor of the ligand is showing 100. How can I justify this issue. Asking for suggestions. Regards, Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient

[ccp4bb] Coot chain ID

Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the Merge Molecules and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B

[ccp4bb] Real Space Refine Zone for Ligand

Dear Crystallographers, After one round of refinement (restrained refinement) with ligand, I inport the .cif file through '-Import CIF Dictionary' into Coot. But when I am going for '-Real Space Refine Zone' for the ligand, its showing Refinement set up failure. Failed to find restrained for:

[ccp4bb] Indexing problem

but the cell parameters are a=67.9, b=82.4, c=91.7. Should I continue with this parameter? What are the other possibilities for indexing? Thanks for your suggestions in advance. Regards, Dipankar Manna This e-mail and any files transmitted with it are for the sole use

[ccp4bb] High chi square value

square value. Does anybody experienced this situation? Thanks in advance. Regards, Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you

[ccp4bb] Same protein showing different SG

Dear All, Recently I collected one data set for the protein having SG P222 with a= 36.8, b= 44.7, c= 78.4(reported with compound). I crystallized the protein with same kind of other compound. The diffraction was up to 2.3A. But I am facing problem during indexing. I tried with SGP222 (as

[ccp4bb] High R factor

%, but when I run rigid body refinement (Refmac5) the Rfactor is showing 46.07% and Rfree is 46.27. is it possible? Or else what I have to do with this data. Please suggest. Regards Dipankar Manna This e-mail and any files transmitted with it are for the sole use

[ccp4bb] How to reduce no. of overlaps

that much. Please give me some suggestions. Regards, Dipankar Dipankar Manna Aurigene Discovery Technologies Limited, #39-40 KIADB Industrial Area, Electronic City, Phase II, Hosur Road, Bangalore- 560 100, India Cell: +91-9538631469 | Office Ph : +91 80-66204422 (Extn: 398) | Email ID: dipanka

[ccp4bb] Restrained refinement problem

Dear All, As I am practicing new in the crystallography, I am facing some difficulties in refining the ligand bound structure. Protein I am working with has SG P212121, it's a dimer. I fitted the ligand on the density with COOT--calculate--Model/Fit/Refine--Rotate/Translate Zone. Then I merged

[ccp4bb] How to reduce R factor

Dear Crystallographers, Can anybody guide me how to reduce R-factor, means which are the basic parameters I have to look for to reduce the R-factor during refinement. I am newly learning the refinement. After running molrep R-factor is around 53% (100% identity), after rigid body refinement

[ccp4bb] Crystal rotation or crystal oscillation or both?

Dear Crystallographers, May be this is a very stupid question- which terminology should we use for crystal data collection- Crystal Rotation or Crystal Oscillation or both? I apologise if this is already discussed! Best, Dipankar -- Dipankar Manna Research Scholar Department of Chemistry

Re: [ccp4bb] Cleaved peptide density!

: Thought about any E.Coli protease as an impurity.. very small quantity? Cheers, Rajesh. On Mon, Apr 20, 2015 at 9:14 PM, Dipankar Manna dipankar.biot...@gmail.com wrote: Dear Barbel, Thank you! Yes you are right that I did the SDS-PAGE with bigger substrate. Regarding peptide, we

Re: [ccp4bb] Cleaved peptide density!

not to be what the label says. Bärbel Zitat von Dipankar Manna dipankar.biot...@gmail.com: Dear Bonsor, Thanks for your suggestions! It need 2-3 weeks to get the fully grown crystals. And harvest, freeze and data collection just take usually next 3-5 days. I usually incubated substrate

[ccp4bb] Cleaved peptide density!

getting the cleaved peptide as I already mutated the active residue Cysteine with Alanine (this mutant did no show any activity when I checked with SDS-PAGE). If anybody has the same kind of experience please advice me. Thanks in advance. Best, Dipankar -- Dipankar Manna Research Scholar

Re: [ccp4bb] Cleaved peptide density!

the course of crystallization. You may want to use fresh beads, or treat columns with pepsin or sodium hydroxide. Not real answers I am afraid, more like suggestions. -- Dipankar Manna Research Scholar Department of Chemistry University of Oslo Oslo, Norway

[ccp4bb] Expressing protein in insect cells

me the further steps. Is it possible that the native signal is necessary for the secretion, even in the insect cell expression? Also what other signal sequences could be used instead of HBM? Thanks in advance for your suggestions/comments! Best, Dipankar -- *Dipankar Manna, Ph.D* Postdoctoral

Re: [ccp4bb] Precipitation issue during refolding

es (refolding, concentration, heating etc). > > Also I would echo the comment about adding in inhibitors - not only can > they prevent proteolysis, but can also stabilise the active site and help > with refolding. > > Good luck with it! > > Tom > > > > > On T

[ccp4bb] Precipitation issue during refolding

, Dipankar​ -- *Dipankar Manna, Ph.D* Postdoctoral Researcher Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo, Domus Medica Oslo, Norway Mob : +47 451 66 517 <451%2066%20517> E-mail: dipankar.ma...@medisin.uio.no <dipankar.ma...@kje