Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

This is why I said this is somewhat subjective. I would agree I/sigI of 0.6+ and cc1/2 of 0.5+ in high res shell is fine but these values are overall, as the resolution range is 23-2.6 angstroms. On Thu, Nov 2, 2023 at 12:16 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Am I confused? I would accept an I/SigI of 1+, and a CC1/2 of 0.5 as pretty acceptable? E On Thu, 2 Nov 2023 at 15:03, Dr. Kevin M Jude wrote: > As suggested by the (conflicting) observations of Eleanor and Nicholas, > it’s not clear whether you are showing data collection statistics for the > f

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Hi Mandar Bhutkar, the data statistics (Rmerge, I/sigma, CC1/2) appear to be poor. So you may want to check the data processing; try with different programs, and perhaps with help from experienced people in your group. You could ask for help here, but you should give more details - what exactly

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

As suggested by the (conflicting) observations of Eleanor and Nicholas, it’s not clear whether you are showing data collection statistics for the full resolution range or just for the high resolution shell. If for the whole dataset, your Rmerge, I/sigma, and CC1/2 are high, low, and low, respect

[ccp4bb] Downtime for PDB-REDO, AlphaFill, DSSP and CCD.

Dear CCP4 and CCPEM bulletin boarders, Due to scheduled electrical maintenance at our host instate, our structural biology resources PDB-REDO (https://pdb-redo.eu), AlphaFill (https://alphafill.eu), DSSP (https://pdb-redo.eu/dssp) and CCD (https://ccd.rhpc.nki.nl/) will be harder to reach from

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Mandar, It would also be helpful if you could share the statistics in the highest resolution shell. But to me (which is admittedly a bit subjective), as noted by Eleanor, the R-merge seems a bit high and the your I/sigma and CC1/2 seem a bit low. Which doesn’t really matter if you can build a reas

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Well - you probably could use data to a higher resolution I/SigI and CC 1/2 are quite high. The better the resolution the better the model usually. On the other hand your Rmerge is high-ish. Hard to comment without seeing the data processing results. Look at the plots of 2nd moment, wilson plot,

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[ccp4bb] AW: [ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage

(this is from a different jon) if a chelator really is necessary at this stage (post AmS?), in any case use IDA instead of EDTA! that's pretty obvious from the affinities of EDTA/NTA/IDA. cheers jon Von: CCP4 bulletin board Im Auftrag von Jonathan Bailey Gesendet: Mittwoch, 1. November 2023 19:5

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Dear Mandar, - you may be able to find some more, less well-ordered, waters by looking at (difference) maps. These will probably refine to have higher B-factors, pushing your average up. - some of your best-ordered water molecules may in fact be metal ions, you can check the coordination. Model

[ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Hi everyone, I am working on one of the x-ray diffraction data. Refinement details are given below. My solvent b factor is 18.44. Can anyone pls suggest me how to improve the data? Thank you. -- Mr. Mandar Bhutkar, Ph.D. student, Molecular Virology lab, IIT Roorkee. Resolution range 23.06–2.60