[ccp4bb] R factor geeting stuck

Hi ccp4 experts, I have collected diffraction images to 0.96 Angstrom resolution to the edge of the detector. One data set give me the full completeness and   below i have pasted my statistic values got from XDS. I have cut off data at 1.12 A  which seems to be quite nice regarding all

Re: [ccp4bb] Lysine coordinated ions

Hi Kaherine, It seems its a modified lysine in to kcx (Carbamylated lysine) but its only the case if you used during entire purification or crystallization BME in your buffer Best Regards AFSHAN On Wednesday, July 2, 2014 5:38 PM, Katherine Sippel katherine.sip...@gmail.com wrote:

[ccp4bb] Hi

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[ccp4bb] having difficulties with ammonium ion

Hello all, I am refining  my structures with REFMAC 5 and is failed. Actually i used ammonium dihydrogen phosphate buffer during crystallization and in the map file where i observed the density of ammonium ion (NH4). I get this ion from the coot library but when i run refmac its failed even i

[ccp4bb] need suggestions

 Dear All, I have encountered one problem to optimization the crystallization condition manually. Actually i got the good shape and even size crystal in a screening plate. The condition are : 20% PEG 6000, 0.1M MES pH 6.0 whereas protein in 10mM Na-acetate pH 5.7 contain 50mM NaCl, 1mM EDTA

[ccp4bb] need proper suggestion

Dear All, I have a severe prob lam to performed my ligand binding study with corresponding protein. I have taking the native diffraction data at 1.75 A and after that i have performed soaking as well co-crystallization experiment with my inhibitors. Problem is that at the active site

[ccp4bb] hello

Dear all,  Could any one help me regarding my serious problem actually i have collected data at 3.0 and cut off 3.1 where the data statics showed the good  values for the further processing.  According to the methew coefficient there would be two molecule in the asymmetric unit but after

[ccp4bb] hello

Dear all, I have facing one problem during the refinement of my protein . Actually in my protein  there are some modified amino acids are present  like Cystein is modified into CME which i can get easily from monomer libraray in coot . but after refinement in Pdb text file  indicated some gaps

[ccp4bb] How can improve diffraction quality

 Dear ccp4 user I am facing one crucial problem regarding diffraction. Actually the size of my crystal is good enough 0.5mm but it  was diffracted only 4 A. The conditions of crystallization recipes are 4.5% PEG 1000, 0.1M Tris and 25mM Na citrate. I really need your suggestions regarding 

[ccp4bb] how can merge two PDB

Hello CCP4 user I have collected a data set 2.1 for my complex. Actually after  first run of Rafmac i can see the density for my inhibitor but the problem is my inhibitor is 6 KDa and i know the sequence of my inhibitor as well this inhibitor already crystallize with other protein molecule

Re: [ccp4bb] how can merge two PDB

it? Best Regards AFSHAN From: Afshan Begum afshan...@yahoo.com To: Bosch, Juergen jubo...@jhsph.edu Sent: Wednesday, October 19, 2011 4:58 PM Subject: Re: [ccp4bb] how can merge two PDB   H.EDU To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, October 19, 2011 4:29

[ccp4bb] chirality problem

Dear Users, I am facing difficulties to validate my structure according to PDB server. I have solved my structure and now want to submit in PDB but during validation process i have  some chirality problem specially   VAL and LEU amino acids there are total 18 amino acids which deviated from

[ccp4bb] Fixing Modified residue

Dear Expert, I have a trouble to fix the lysin modified residue in to the PDB coordinate.  what i did,I get the KCX(Modified lysin) coordinate from monomer library in COOT (0.9) , merge in to the coordinate file , its listed into position 193 lysin then  run rafmac 5 , its place the residue but

[ccp4bb] Hello

Hi Experts,  I have a problem to see the residue information on COOT if I click on residue info and place the curser their its just blink and disappear as I want to reduce some occupancy manually and it did not work but for water and the other stuff its work completely fine but not for the

[ccp4bb] Need suggestion

st Regards ======= Afshan Begum To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jisc