We should all thank you mandar for stimulating our thinking and setting off a thoughtful discussion!
This is perfectly publishable - st 2,6A placing water molecules is a bit problematic and you will probably only see clearly the well ordered solvent hence the lower average b factor. Just a pointer for all contributors to the BB, it helps to give the resolution of your data up front. Sensible comment is easier then.. Good luck with your writing up. Eleanor On Fri, 3 Nov 2023 at 07:11, Mandar Bhutkar < [email protected]> wrote: > Dear all, I want to express my gratitude for all your valuable > suggestions. I would like to apologize for any confusion that may have > arisen regarding the R merge number. Please understand that I am relatively > new to this field and have a basic understanding, which may sometimes lead > to using layman's terms. I've updated the data refinement table for your > reference. The values in parentheses pertain to the highest-resolution > shell. I plan to implement the suggestions provided in the previous email. > I've noticed that out of 124 water molecules, only 19 have a B-factor of 30 > or above. However, when I examine the difference map, it appears that the > density for all 124 has been appropriately weighted. (Earlier, there was a > distinction between green and blue densities, but after adding water, it's > consistently blue.) You can refer to the attached images for contour levels > from the refinement (1.0 rmsd) and difference map (2.5 rmsd). > > Previously, I attempted to manually fill in water densities, which > unfortunately resulted in a higher R-free value. I will continue to work on > the valuable suggestions provided by all of you. However, if I'm unable to > improve the model further, I have a few queries: > > Is it necessary to include solvent B-factors in the refinement table? I've > observed that many low-resolution structure articles do not provide this > data. > Is the data publishable? For instance, in 2018, PDB ID: 5YIG was published > in EJMC. > How can I justify the lower solvent B-factor?" > I hope this revised version helps convey your message more clearly. > Thank you. > > *Resolution range* > > 23.06–2.60 (2.72- 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 (%)* > > 99.6 (99.3) > > *R**merge* a > > 0.168 (0.372) > > *I/σ(I)* > > 7.3 (3.3) > > *CC(1/2)* > > 0.977 (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 > > On Fri, Nov 3, 2023 at 2:44 AM Nicholas Clark < > [email protected]> wrote: > >> 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 < >> [email protected]> 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 <[email protected]> >>> 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 <[email protected]> on behalf of >>>> Mandar Bhutkar <[email protected]> >>>> *Date: *Thursday, November 2, 2023 at 12:34 AM >>>> *To: *[email protected] <[email protected]> >>>> *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 >> > > > -- > Mr. Mandar Bhutkar, > Ph.D. student, > Molecular Virology lab, > IIT Roorkee. > > ------------------------------ > > 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/
