Re: [ccp4bb] Careless and negative Wilson B-factor

Fri, 06 Jan 2023 06:38:53 -0800

Dear Jon,


The data were obtained from a single crystal.


Gyuhyeok

--------- 원본 메일 ---------
보낸사람 : Jon Cooper <[email protected]>
받는사람 : <[email protected]>
받은날짜 : 2023/Jan/6(Fri) 21:48:21
제목 : Re: [ccp4bb] Careless and negative Wilson B-factor
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


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-------- 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)





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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]




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