Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

被引：3522

作者：

Liebschner, Dorothee ^{[1
]}

Afonine, Pavel V. ^{[1
]}

Baker, Matthew L. ^{[2
]}

Bunkoczi, Gabor ^{[3
,10
]}

Chen, Vincent B. ^{[4
]}

Croll, Tristan I. ^{[3
]}

Hintze, Bradley ^{[4
,11
]}

Hung, Li-Wei ^{[5
]}

Jain, Swati ^{[4
,12
]}

McCoy, Airlie J. ^{[3
]}

Moriarty, Nigel W. ^{[1
]}

Oeffner, Robert D. ^{[3
]}

Poon, Billy K. ^{[1
]}

Prisant, Michael G. ^{[4
]}

Read, Randy J. ^{[3
]}

Richardson, Jane S. ^{[4
]}

Richardson, David C. ^{[4
]}

Sammito, Massimo D. ^{[3
]}

Sobolev, Oleg V. ^{[1
]}

Stockwell, Duncan H. ^{[3
]}

Terwilliger, Thomas C. ^{[5
,6
]}

Urzhumtsev, Alexandre G. ^{[3
,7
,8
]}

Videau, Lizbeth L. ^{[4
]}

Williams, Christopher J. ^{[4
]}

Adams, Paul D. ^{[1
,9
]}

机构：

[1] Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA

[2] Baylor Coll Med, Verna & Marrs McLean Dept Biochem & Mol Biol, Houston, TX 77030 USA

[3] Univ Cambridge, Cambridge Inst Med Res, Dept Haematol, Cambridge CB2 0XY, England

[4] Duke Univ, Dept Biochem, Durham, NC 27710 USA

[5] ELos Alamos Natl Lab, Los Alamos, NM 87545 USA

[6] New Mexico Consortium, Los Alamos, NM 87544 USA

[7] UdS, Ctr Integrat Biol, Inst Genet & Biol Mol & Cellulaire, CNRS,INSERM, F-67404 Illkirch Graffenstaden, France

[8] Univ Lorraine, Fac Sci & Technol, BP 239, F-54506 Vandoeuvre Les Nancy, France

[9] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA

[10] Astex Therapeut Ltd, Cambridge CB4 0QA, England

[11] Duke Univ, Med Ctr, Duke Inst Hlth Innovat, Durham, NC 27701 USA

[12] NYU, Dept Chem, New York, NY 10003 USA

来源：

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2019年 / 75卷

基金：

美国国家卫生研究院; 英国惠康基金;

关键词：

Phenix; automation; macromolecular crystallography; cryo-EM; X-rays; neutrons; diffraction; !text type='Python']Python[!/text; cctbx; C plus plus; CRYO-EM; MOLECULAR-REPLACEMENT; STRUCTURE VALIDATION; DENSITY MODIFICATION; NUCLEIC-ACIDS; SERIAL CRYSTALLOGRAPHY; GEOMETRIC PARAMETERS; STRUCTURE REFINEMENT; PROTONATION STATE; BACKBONE GEOMETRY;

D O I：

10.1107/S2059798319011471

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

引用

页码：861 / 877

页数：17

共 157 条

[1]

Abrahams D., 2003, C/C++ Users Journal, V21, P29

[2] Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB) [J].

Adams, Paul D. ;

Afonine, Pavel V. ;

Baskaran, Kumaran ;

Berman, Helen M. ;

Berrisford, John ;

Bricogne, Gerard ;

Brown, David G. ;

Burley, Stephen K. ;

Chen, Minyu ;

Feng, Zukang ;

Flensburg, Claus ;

Gutmanas, Aleksandras ;

Hoch, Jeffrey C. ;

Ikegawa, Yasuyo ;

Kengaku, Yumiko ;

Krissinel, Eugene ;

Kurisu, Genji ;

Liang, Yuhe ;

Liebschner, Dorothee ;

Mak, Lora ;

Markley, John L. ;

Moriarty, Nigel W. ;

Murshudov, Garib N. ;

Noble, Martin ;

Peisach, Ezra ;

Persikova, Irina ;

Poon, Billy K. ;

Sobolev, Oleg V. ;

Ulrich, Eldon L. ;

Velankar, Sameer ;

Vonrhein, Clemens ;

Westbrook, John ;

Wojdyr, Marcin ;

Yokochi, Masashi ;

Young, Jasmine Y. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2019, 75 :451-454

[3] PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].

Adams, Paul D. ;

Afonine, Pavel V. ;

Bunkoczi, Gabor ;

Chen, Vincent B. ;

Davis, Ian W. ;

Echols, Nathaniel ;

Headd, Jeffrey J. ;

Hung, Li-Wei ;

Kapral, Gary J. ;

Grosse-Kunstleve, Ralf W. ;

McCoy, Airlie J. ;

Moriarty, Nigel W. ;

Oeffner, Robert ;

Read, Randy J. ;

Richardson, David C. ;

Richardson, Jane S. ;

Terwilliger, Thomas C. ;

Zwart, Peter H. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221

[4] Recent developments in phasing and structure refinement for macromolecular crystallography [J].

Adams, Paul D. ;

Afonine, Pavel V. ;

Grosse-Kunstleve, Ralf W. ;

Read, Randy J. ;

Richardson, Jane S. ;

Richardson, David C. ;

Terwilliger, Thomas C. .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2009, 19 (05) :566-572

[5] Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules [J].

Adams, Paul D. ;

Mustyakimov, Marat ;

Afonine, Pavel V. ;

Langan, Paul .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2009, 65 :567-573

[6] PHENIX:: building new software for automated crystallographic structure determination [J].

Adams, PD ;

Grosse-Kunstleve, RW ;

Hung, LW ;

Ioerger, TR ;

McCoy, AJ ;

Moriarty, NW ;

Read, RJ ;

Sacchettini, JC ;

Sauter, NK ;

Terwilliger, TC .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 :1948-1954

[7] Bulk-solvent and overall scaling revisited: faster calculations, improved results [J].

Afonine, P. V. ;

Grosse-Kunstleve, R. W. ;

Adams, P. D. ;

Urzhumtsev, A. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2013, 69 :625-634

[8] On macromolecular refinement at subatomic resolution with interatomic scatterers [J].

Afonine, Pavel V. ;

Grosse-Kunstleve, Ralf W. ;

Adams, Paul D. ;

Lunin, Vladimir Y. ;

Urzhumtsev, Alexandre .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2007, 63 :1194-1197

[9] New tools for the analysis and validation of cryo-EM maps and atomic models [J].

Afonine, Pavel V. ;

Klaholz, Bruno P. ;

Moriarty, Nigel W. ;

Poon, Billy K. ;

Sobolev, Oleg V. ;

Terwilliger, Thomas C. ;

Adams, Paul D. ;

Urzhumtsev, Alexandre .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2018, 74 :814-840

[10] From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation [J].

Afonine, Pavel V. ;

Adams, Paul D. ;

Urzhumtsev, Alexandre .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2018, 74 :621-631

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