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

[조규혁]

Dear Eleanor,

I was wondering if the model and structure factors with the negative Wilson B-factor can be deposited in the PDB or made interpretable for biochemical experiments.

The data were initially processed in XDS and the CORRECT output (XDS_ASCII.HKL) was provided to Careless.

Sincerely,

Gyuhyeok

--------- 원본 메일 ---------

보낸사람 : Eleanor Dodson <eleanor.dod...@york.ac.uk>
받는사람 : <gyuhyeok...@gist.ac.kr>
참조 : <CCP4BB@jiscmail.ac.uk>
받은날짜 : 2023/Jan/6(Fri) 20:09:57
제목 : Re: [ccp4bb] Careless and negative Wilson B-factor

The tool must have sharpened your data - sometimes enhancing the outer data does improve the electron density..

So I wouldnt worry about that "negative" B factor - it is doubtless a result of the "careless" run, and not presumably the one you got at the data processing step..

Eleanor

On Fri, 6 Jan 2023 at 08:27, "조규혁" <gyuhyeok...@gist.ac.kr> 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: gyuhyeok...@gist.ac.kr

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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: gyuhyeok...@gist.ac.kr

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