Hi Liliana, Two things leap out at me when I look at your data summary.
(1) Your data probably do not go to 1.77Å. The CC1/2 in your outer shell is below any of the usual thresholds. There are discussions to be had about what the threshold is, but normally CC1/2 values of 0.5 or sometimes 0.3 are used. You should also consider I/sigI. (2) I believe that by default Phenix.refine excludes weaker reflections from refinement, which leads to the discrepancy in completeness statistics. As your data do not extend as far as what is contained in your mtz file, Phenix excludes those essentially "empty" reflections. Judging by the Phenix refine output, I would estimate your data goes to somewhere around 1.9Å The program Pairef can help inform your choice of high-resolution cutoff. This can be run from CCP4cloud, but is also available for Phenix, I believe. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248825/ Hope this helps, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs<http://about.me/david_briggs> ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Liliana Margent <lmarg...@gradcenter.cuny.edu> Sent: Wednesday, January 17, 2024 9:19:36 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Resolution Discrepancy in Data Set External Sender: Use caution. Hello all, I hope this message finds you well. In my current data set, I’ve encountered a discrepancy between the completeness in the high-resolution shells in merged statistics vs the refinement statistics. For example, when I look at my merged statistics file, output by Xia2 dials, the completeness in the high-resolution shells are 97.6%. When I take this data and subsequently refine it in PHENIX I get extremely different completeness ranges in the high-resolution shells, but I cannot figure out why this large difference is occurring. I’m reaching out to you, our esteemed community, for any insights or advice you might have. Has anyone else faced a similar challenge? If so, how did you navigate through it? Your experiences and suggestions could be invaluable in helping me understand and resolve this issue. Thank you in advance for your time and expertise. Best regards, Liliana see a side-by-side image of the files I mention in the message in https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1Y783MzlnqVwXRCtiLeV0Y2EpmkeDL2nd%2Fview%3Fusp%3Dsharing&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5XcApcqvUkuvjz9oGUsaFpvnfY2p2X1LDE8G4XhFkuo%3D&reserved=0<https://drive.google.com/file/d/1Y783MzlnqVwXRCtiLeV0Y2EpmkeDL2nd/view?usp=sharing> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gS2JOO3L%2BYCu2GmMo6I9ajQZn9ZiyZTLzYEZ7CfJN2Q%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=y27c8QI3JX%2BYozm2TcSLZlj%2Fo2rOxLUhAJAdwxpxzp8%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sJz0AxBNJb5PxOlNT9%2FKN9MobG2EKXURC67CNB4qbnE%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KIkPxpkW00RhNR7ODU%2F1EFLtP6HAd5Jg2r2K5bUC9Tc%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT ######################################################################## 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/
