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. Modeling these as metal will then remove some waters with likely very low B-factors, also leading to a higher average B-factor for the remaining water molecules. Check My Metal may be useful: https://cmm.minorlab.org
But: - it shouldn't really be a goal to increase the B-factor of the solvent, but to find and model all the water molecules (metal ions, protein and everything else) with reasonable density and hydrogen bonds. - when you write "improve the data", I assume you mean "improve the model". Best wishes, Mark Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 2 Nov 2023, at 08:24, Mandar Bhutkar > <0000b29d954423ab-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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 > <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/
