Dear Jon and Gyuhyeok the real connaisseurs (e.g. Kay Diedrichs, et al) will certainly respond much better to this! Redundancy is really high here (which is good of course), likely explaining the high-ish Rmerge. Indeed, “redundancy-aware“ indices, like Rpim, are much better, and actually quite good overall :)
It is true that Rmeas (with also integrates multiplicity), does diverge quite a bit from Rpim. As far as I recall the difference between these two being that the former reports on individual measurements, whilst Rpim uses merged data. Why that difference among them? Kay? In any case, with >40 multiplicity, Rpim looks pretty good (and, consistent with CCs, makes sense) Best, Alejandro > On 6 Jan 2023, at 09:47, Jon Cooper > <[email protected]> wrote: > > Hello, are the data from serial crystallography? The redundancy and the CC's > are very good but the R-merge (an unpopular metric these days) is quite high? > > Cheers, Jon Cooper2 > > > Sent from ProtonMail mobile > > > > -------- Original Message -------- > On 6 Jan 2023, 08:17, 조규혁 < [email protected]> wrote: > > Dear all, > > I recently tested a novel merging tool for crystallography data called > Careless (https://github.com/rs-station/careless). > > When I used it on our 2.6 A-resolution structure in the I23 space group with > a lipid bound structure, I noticed that the electron density surrounding the > acyl chain was significantly improved. > > However, I am concerned about the Wilson B-factor. The Phenix.table_one tool > reports that the Wilson B-factor of the merged mtz file is -0.91. > Phenix.Xtriage warns that a negative Wilson B-factor can be an indication of > unusual pathology or artificial manipulation. > > Has anyone else encountered similar conditions? Are there any circumstances > in which a negative Wilson B-factor can be rationalized? > > Thank you, > Gyuhyeok > > > > P.S. Here is the part of the output of Phenix.table_one. > > > > Wavelength 1.0000 > Resolution range 37.98 - 2.60 > (2.69 - 2.60) > Space group I 2 3 > Unit cell 161.128 161.128 161.128 > 90 90 90 > Total reflections 886846 (79364) > Unique reflections 21520 (2135) > Multiplicity 41.2 (37.2) > Completeness (%) 99.95 (100.00) > Mean I/sigma(I) > 14.2 (0.8) > > Wilson B-factor -0.91 > R-merge 0.240 (4.566) > R-meas 0.243 (4.629) > R-pim 0.038 (0.757) > CC1/2 0.998 (0.362) > CC* 0.999 (0.729) > > > > > > > > > PhD student > > Department of Chemistry > > Gwangju Institute of Science and Technology (GIST) > > 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005 > Republic of Korea > > Tel. +82 62-715-4633 > > e-mail: [email protected] > > > > > > 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/
