DOI: 10.1110/ps.0350503. Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein

Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein–nucleic acid complex crystals

10.1110/ps.0350503

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractEstimating the number of molecules in the crystallographic asymmetric unit is one of the first steps in a macromolecular structure determination. Based on a survey of 15,641 crystallographic Protein Data Bank (PDB) entries the distribution of VM, the crystal volume per unit of protein molecular weight, known as Matthews coefficient, has been reanalyzed. The range of values and frequencies has changed in the 30 years since Matthews first analysis of protein crystal solvent content. In the statistical analysis, complexes of proteins and nucleic acids have been treated as a separate group. In addition, the VM distribution for nucleic acid crystals has been examined for the first time. Observing that resolution is a significant discriminator of VM, an improved estimator for the probabilities of the number of molecules in the crystallographic asymmetric unit has been implemented, using resolution as additional information.

Bibliography

Kantardjieff, K. A., & Rupp, B. (2003). Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and proteinânucleic acid complex crystals. Protein Science, 12(9), 1865â1871. Portico.

Authors 2

Katherine A. Kantardjieff (first)
Bernhard Rupp (additional)

References 18 Referenced 571

10.1016/S0076-6879(85)17007-2
10.1093/nar/28.1.235
10.1002/bip.1968.360060805
10.1007/BFb0115599
{'key': 'e_1_2_7_6_1', 'volume-title': 'Clustering algorithms', 'author': 'Hartigan J.', 'year': '1975'} / Clustering algorithms by Hartigan J. (1975)
{'key': 'e_1_2_7_7_1', 'volume-title': 'Applied discriminant analysis', 'author': 'Huberty C.J.', 'year': '1994'} / Applied discriminant analysis by Huberty C.J. (1994)
{'key': 'e_1_2_7_8_1', 'volume-title': 'Statistical analysis', 'author': 'Kachigan S.K.', 'year': '1986'} / Statistical analysis by Kachigan S.K. (1986)
10.4135/9781412983938
10.1016/0022-2836(68)90205-2
10.1146/annurev.pc.27.100176.002425
10.1111/j.1432-1033.1986.tb09653.x
10.1051/epn:2002401
10.1016/S0076-6879(85)17006-0
{'key': 'e_1_2_7_15_1', 'first-page': '791', 'article-title': 'Accurate calulation of the density of proteins', 'volume': '56', 'author': 'Quillin M.L.', 'year': '2000', 'journal-title': 'Acta Crystallogr.'} / Acta Crystallogr. / Accurate calulation of the density of proteins by Quillin M.L. (2000)
{'key': 'e_1_2_7_16_1', 'volume-title': 'Cluster analysis', 'author': 'Tryon R.C.', 'year': '1939'} / Cluster analysis by Tryon R.C. (1939)
{'key': 'e_1_2_7_17_1', 'volume-title': 'Cluster analysis', 'author': 'Tryon R.C.', 'year': '1973'} / Cluster analysis by Tryon R.C. (1973)
10.1016/0165-022X(80)90055-X
10.1038/nsb1295-1062

Dates

Type	When
Created	21 years, 11 months ago (Aug. 27, 2003, 6:42 p.m.)
Deposited	1 year, 10 months ago (Sept. 28, 2023, 10:11 a.m.)
Indexed	1 day, 11 hours ago (Aug. 22, 2025, 12:45 a.m.)
Issued	21 years, 11 months ago (Sept. 1, 2003)
Published	21 years, 11 months ago (Sept. 1, 2003)
Published Online	16 years, 7 months ago (Jan. 1, 2009)
Published Print	21 years, 11 months ago (Sept. 1, 2003)

Funders 0

None

BibTeX

@article{Kantardjieff_2003, title={Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein–nucleic acid complex crystals}, volume={12}, ISSN={1469-896X}, url={http://dx.doi.org/10.1110/ps.0350503}, DOI={10.1110/ps.0350503}, number={9}, journal={Protein Science}, publisher={Wiley}, author={Kantardjieff, Katherine A. and Rupp, Bernhard}, year={2003}, month=sep, pages={1865–1871} }

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