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 <kj...@stanford.edu> wrote: > 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, > respectively; if for the high resolution shell, they suggest that you > should include higher resolution data in your refinement, if available. > > > > See https://doi.org/10.1107/S0907444913000061 and > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/, and for the > standard format of reporting these statistics see any crystal structure > reported in Acta Cryst D. > > > > Best wishes > > Kevin > > > > *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Mandar > Bhutkar <0000b29d954423ab-dmarc-requ...@jiscmail.ac.uk> > *Date: *Thursday, November 2, 2023 at 12:34 AM > *To: *CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject: *[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* > > *Space group* > > P 2 21 21 > > *Unit cell dimensions: a b c (Å)* > > *α, β, γ (°)* > > 51.6 60.7 184.36 > 90 90 90 > > *Completeness (%)* > > 99.3 > > *Rmerge a* > > 0.372 > > *I/σ(I)* > > 2.67 > > *CC(1/2)* > > 0.773 > > *Refinement* > > *Reflections used in refinement* > > 10011 > > *Reflections used for R-free* > > 924 > > *R-workb* > > 0.231 > > *R-freeb* > > 0.273 > > *Wilson B-factor (Å)* > > 28.9 > > *Number of non-hydrogen atoms* > > 4302 > > *Macromolecules* > > 4086 > > *Ligands* > > 94 > > *Solvent* > > 124 > > *Protein residues* > > 508 > > *RMS (bonds) (Å)c* > > 0.01 > > *RMS (angles) (˚) c* > > 1.89 > > *Ramachandran Plot* > > > > *Favored (%)* > > 97.83 > > *Allowed (%)* > > 1.38 > > *Outliers (%)* > > 0.79 > > *Average B-factor (Å)* > > 28.0 > > *macromolecules (Å)* > > 28.65 > > *ligands (Å)* > > 48.98 > > *solvent (Å)* > > 18.44 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
