[ccp4bb] Protein Purification

Dear All I am purifying a protein from liver. In first step I spotted protein in Flow Through and could see intense band in SDS PAGE. I pooled the fraction and did second column. Surprisingly I could not see UV absorbance or even any band in the SDS. I used PMSF as protease inhibitor from begin

[ccp4bb] ITC thermogram

Dear All I am running ITC experiment for my protein. At 250 nm Ligand concentration (protein was 40nm) I was getting exothermic thermogram. But it was not saturated. I reduced Ligand concentration to 15 nm and checked again. I got endothermic thermogram. I dont understand why I am getting both

[ccp4bb] ITC with heterogeneous protein

Dear All, This is an off-topic question. I have protein solution of heterogeneous (contains both monomer and dimer). I want to perform ITC with this protein. I doubt whether this heterogeneity will interfere the binding study. Any advice please. Thank you Sajid

[ccp4bb] column profile

Hi all If anyone have, please post the calibration profile for GE Sephacryl S100 26/60 Hiprep column. Sorry I could not locate in the GE Healthcare site. Thankx in advance Sajid

Re: [ccp4bb] NADP behaviour in crystal

From: Christina Bourne To: sajid akthar Sent: Thu, 29 April, 2010 4:53:50 PM Subject: Re: [ccp4bb] NADP behaviour in crystal Maybe the soak wasn't successful? NADP usually sits in a groove that may not be accessible in your crystal form; perhaps it's just sticking

[ccp4bb] NADP behaviour in crystal

Hi All I had a soaked crystal with NADP; and the crystal diffracted to 2.5A. I was looking for NADP at its binding site, I came up with wierd density which I could not fit with any end of NADP. The density is upto 3.5 A in Fo-Fc map; and is spherical long enough to put nicotine. But the density

[ccp4bb] NADP - ADP binding

Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek

[ccp4bb] Peg3350 model

Hi All I have some density and I can fit a peg molecule in their. I am confused and when I search database for peg3350, I have no hit. How can I build a model for Peg 3350. I found some PDB's with peg; but they they have used peg400; Is there any difference in the model between peg3350 and peg4

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Dear All Is there any easy to way write topology and parameter file for a cofactor with specific conformation. Thanks a lot Sajid Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com

[ccp4bb]

Hi all I have used NADP in my crystallisation condition; and the crystal diffracted well; I built the model completely and the r-factor and r-free are 0.26 and 0.29 respectively. The resolution is 2.3A. I am looking for NADP, in the binding region; I could see some density for NADP; But it is n

[ccp4bb] Auto Sharp - problem

Hi all I am trying to run autoSHARP. When I submit the job I got following message and the job is not running. Does any one have got error like this when you start autoSHARP Any advice please Sajid ** (In case of remotel

[ccp4bb] mrBUMP - proxy to internet

Dear All I want to run MrBump. We have dynamic internet system in our institute. So I am not able to locate the proxy address. Any help please Sajid From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/

[ccp4bb] Cool - Clipper installation

Dear All I had installed coot on my red hat system. For some reason it has been deleted. I'm trying to install again. Before that Do I need to install "clipper". When I'm trying to install clipper it says error message like --- configure: error: If fftw ex

Re: [ccp4bb] crystallisation

Dear All Thank you for your suggestions. I got many suggestions from you. Due to my time constraint, I'm not writing summary, but some replies for your suggestions to my previous query. I have not mentioned fully what I tried to do better diffraction. I'm listing them here which were mentioned b

[ccp4bb] phasing at low resolution

Hi All I have a data set of Se-Met crystal 3.65A resolution collected at Inflection and peak wavelength. Also I have a data set at same resolution in native form. The protein size is 28000 dalton. I dont have any model for this protein. So I started to find the heavy atom peak search to find out

[ccp4bb] refmac5

Dear All Thanks for your suggestions to run revise. Suggestions from Mike Latchem helped me to overcome the problem. I have another question. I am trying to run REFMAC5. It is giving some warning message. # There is no file name for parameter MAPOUT1 The CCP4 program is la

[ccp4bb] Revise

Dear All I'm trying to locate heavy atoms. SO I started with Revise from CCP4. But it fails with error message #CCP4I TERMINATION STATUS 0 " REVISE: Duplicate column labels in output file" #CCP4I TERMINATION TIME 15 Apr 2008 14:50:34 #CCP4I MESSAGE Task failed Any help pls Thanks Sajid

[ccp4bb] Potassium Nitrate

Hi All Sorry for non CCP4 question. I want to make Pottasium Nitrate solution of pH 6.9 (ofcourse for crystallisation trails only). I'm adjusting pH by using NaOH. But it seems the pH is not stable after sometime. Is there any good way to do it. Thank you Sajid Now you can chat withou

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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, still no change. So I'm trying with mineral oil. Here I'm getting some