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 < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1107%2FS0907444913000061&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Ce3442991ca9847fe03bb08dbdbbf0bb4%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345385963446284%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=al5DRQsmmcm2W5GbSYVlLdRQ%2F1WD%2B33deAPiSKyhT3Y%3D&reserved=0> >> and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/ >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3457925%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Ce3442991ca9847fe03bb08dbdbbf0bb4%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345385963602519%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1do%2FaKfwAQOBcbt4z3qsFpHI2f4jg3En0%2B%2F3rrBxujk%3D&reserved=0>, >> 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 >> <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%7Ce3442991ca9847fe03bb08dbdbbf0bb4%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345385963602519%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Iq69qHaU%2B1Uy4uCMqUQAHgxWpD24xNZ29FuwuSrH1fc%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%7Ce3442991ca9847fe03bb08dbdbbf0bb4%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345385963602519%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Iq69qHaU%2B1Uy4uCMqUQAHgxWpD24xNZ29FuwuSrH1fc%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%7Ce3442991ca9847fe03bb08dbdbbf0bb4%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638345385963602519%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Iq69qHaU%2B1Uy4uCMqUQAHgxWpD24xNZ29FuwuSrH1fc%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/
