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, Rmerge v Batch, and read the report carefu;ly. Is there serious radiation damage, should some batches be excluded etc, etc? You may be able to check the anomalous difference maps to see if "waters" are CL or some other metal .. Good luck Eleanor On Thu, 2 Nov 2023 at 08:14, Mark J. van Raaij <[email protected]> wrote: > 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 < > [email protected]> 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 > > > > ------------------------------ > > 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/
