Dear Eleanor,
I agree that the decrease in the B-factor is likely due to "Careless."
The author of this article seems to recognize Wilson B-factor issues during the peer review process (https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-022-35280-8/MediaObjects/41467_2022_35280_MOESM2_ESM.pdf) and offers some options for addressing them (such as the --wilson-prior-b WILSON_PRIOR_B option).
It may take some time for me to get the software running correctly.
Gyuhyeok
P.S. I have attached some preliminary statistics using datasets from Careless or Aimless. Please note that both the Atomic B-factor and the Wilson B-factor are significantly reduced in Careless data.
| Merging tool |
Carelss | Aimless |
| Wavelength | 1.0000 | 1.0000 |
| Resolution range | 37.98 - 2.60 |
43.06 - 2.60 |
| Space group | I 2 3 | I 2 3 |
| Unit cell | 161.128 161.128 161.128 90 90 90 |
161.128 161.128 161.128 90 90 90 |
| Total reflections | 886846 (79364) | 886852 (79364) |
| Unique reflections | 21520 (2135) | 21522 (2135) |
| Multiplicity | 41.2 (37.2) | 41.2 (37.2) |
| Completeness (%) | 99.95 (100.00) | 99.94 (99.95) |
| Mean I/sigma(I) | 14.2 (0.8) | 14.2 (0.8) |
| Wilson B-factor | -0.91 | 74.5 |
| R-merge | 0.240 (4.566) | 0.240 (4.566) |
| R-meas | 0.243 (4.629) | 0.243 (4.629) |
| R-pim | 0.038 (0.757) | 0.038 (0.757) |
| CC1/2 | 0.998 (0.362) | 0.997 (0.362) |
| CC* | 0.999 (0.729) | 0.999 (0.729) |
| Reflections used in refinement | 21520 (2135) | 21519 (2134) |
| Reflections used for R-free | 1118 (112) | 1118 (112) |
| R-work | 0.2027 (0.2547) | 0.2093 (0.3422) |
| R-free | 0.2601 (0.3282) | 0.2564 (0.3634) |
| CC(work) | 0.664 (0.708) | 0.919 (0.622) |
| CC(free) | 0.622 (0.569) | 0.766 (0.478) |
| Number of non-hydrogen atoms | 3930 | 3740 |
| macromolecules | 3655 | 3655 |
| ligands | 72 | 72 |
| solvent | 203 | 13 |
| Protein residues | 443 | 443 |
| RMS(bonds) | 0.008 | 0.009 |
| RMS(angles) | 1.030 | 1.110 |
| Ramachandran favored (%) | 95.4 | 93.2 |
| Ramachandran allowed (%) | 4.3 | 6.4 |
| Ramachandran outliers (%) | 0.2 | 0.5 |
| Rotamer outliers (%) | 2.0 | 3.3 |
| Clashscore | 8.95 | 8.41 |
| Average B-factor | 19.9 | 70.2 |
| macromolecules | 19.7 | 70.0 |
| ligands | 31.1 | 81.5 |
| solvent | 20.1 | 61.5 |
보낸사람 : Eleanor Dodson <[email protected]>
받는사람 : <[email protected]>
받은날짜 : 2023/Jan/8(Sun) 10:39:39
제목 : Re: [ccp4bb] Careless and negative Wilson B-factorI suppose so, but I would refine your final model against the initial data too, and see what R factors you get..EleanorDear 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 <[email protected]>
받는사람 : <[email protected]>
참조 : <[email protected]>
받은날짜 : 2023/Jan/6(Fri) 20:09:57
제목 : Re: [ccp4bb] Careless and negative Wilson B-factorThe 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..EleanorDear 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 90Total 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, 61005Republic of Korea
Tel. +82 62-715-4633
e-mail: [email protected]
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PhD student
Department of Chemistry
Gwangju Institute of Science and Technology (GIST)
123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005Republic of Korea
Tel. +82 62-715-4633
e-mail: [email protected]
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