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 reasonable, high quality model from the data.
What specifically is your concern? Your R-factors (again, in my opinion) seem “ok” for the resolution. The largest issue I see in your statistics is a high percentage of Rakmachandran outliers. More help can be provided depending on what you’re specifically looking to improve. Best, Nick Clark On Thu, Nov 2, 2023 at 6:57 AM Eleanor Dodson < [email protected]> wrote: > 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 >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcmm.minorlab.org%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd70ab0faa0d64f3ebefc08dbdb9263a3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345194592830690%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CbcrgMKcvwoAxb1KWHNxR%2FDuWXnE3iu4cZz%2B6fxBvQg%3D&reserved=0> >> >> 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 >> <https://www.google.com/maps/search/calle+Darwin+3+E-28049+Madrid,+Spain?entry=gmail&source=g> >> E-28049 Madrid, Spain >> <https://www.google.com/maps/search/calle+Darwin+3+E-28049+Madrid,+Spain?entry=gmail&source=g> >> 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 >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd70ab0faa0d64f3ebefc08dbdb9263a3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345194592830690%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ncd0piJrmK7nCplVf8n6FgZ4qRXtaxp4o9iinRr8yh0%3D&reserved=0> >> >> >> >> ------------------------------ >> >> 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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd70ab0faa0d64f3ebefc08dbdb9263a3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345194592830690%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ncd0piJrmK7nCplVf8n6FgZ4qRXtaxp4o9iinRr8yh0%3D&reserved=0> >> > > ------------------------------ > > 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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd70ab0faa0d64f3ebefc08dbdb9263a3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345194592830690%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ncd0piJrmK7nCplVf8n6FgZ4qRXtaxp4o9iinRr8yh0%3D&reserved=0> > ######################################################################## 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/
