Towards automated crystallographic structure refinement with phenix.refine

被引：4378

作者：

Afonine, Pavel V. ^{[1
]}

Grosse-Kunstleve, Ralf W. ^{[1
]}

Echols, Nathaniel ^{[1
]}

Headd, Jeffrey J. ^{[1
]}

Moriarty, Nigel W. ^{[1
]}

Mustyakimov, Marat ^{[2
,3
]}

Terwilliger, Thomas C. ^{[2
,3
]}

Urzhumtsev, Alexandre ^{[4
]}

Zwart, Peter H. ^{[1
]}

Adams, Paul D. ^{[1
,5
]}

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA

[2] Los Alamos Natl Lab, Los Alamos, NM 87545 USA

[3] CNRS INSERM UdS, IGBMC, F-67404 Illkirch Graffenstaden, France

[4] Univ Henri Poincare, Fac Sci & Technol, Dept Phys, F-54506 Vandoeuvre Les Nancy, France

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

来源：

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2012年 / 68卷

关键词：

REAL-SPACE REFINEMENT; ELECTRON-DENSITY MAPS; X-RAY-DIFFRACTION; FREE R-VALUE; CRYSTAL-STRUCTURE; PROTEIN-STRUCTURE; MACROMOLECULAR REFINEMENT; STRUCTURE VALIDATION; THERMAL-MOTION; DATA-BANK;

D O I：

10.1107/S0907444912001308

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

引用

页码：352 / 367

页数：16

共 140 条

[51]

Grosse-Kunstleve R. W., 2010, COMPUT CRYSTALLOGR N, V1, P4

[52]

Grosse-Kunstleve R. W., 2009, ASME C P, V4, P1477

[53] Exact direct-space asymmetric units for the 230 crystallographic space groups [J].

Grosse-Kunstleve, Ralf W. ;

Wong, Buddy ;

Mustyakimov, Marat ;

Adams, Paul D. .

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2011, 67 :269-275

[54] On the handling of atomic anisotropic displacement parameters [J].

Grosse-Kunstleve, RW ;

Adams, PD .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2002, 35 :477-480

[55] The Computational Crystallography Toolbox:: crystallographic algorithms in a reusable software framework [J].

Grosse-Kunstleve, RW ;

Sauter, NK ;

Moriarty, NW ;

Adams, PD .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2002, 35 :126-136

[56]

GROSSEKUNSTLEVE RW, 2004, IUCR COMPUT COMM NEW, V3, P22

[57]

GROSSEKUNSTLEVE RW, 2005, IUCR COMPUT COMMISSI, V5, P69

[58] High-resolution neutron structure of nicotinamide adenine dinucleotide [J].

Guillot, B ;

Lecomte, C ;

Cousson, A ;

Scherf, C ;

Jelsch, C .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2001, 57 :981-989

[59] Crystal structure of cathepsin X: a flip-flop of the ring of His23 allows carboxy-monopeptidase and carboxy-dipeptidase activity of the protease [J].

Guncar, G ;

Klemencic, I ;

Turk, B ;

Turk, V ;

Karaoglanovic-Carmona, A ;

Juliano, L ;

Turk, D .

STRUCTURE, 2000, 8 (03) :305-313

[60] Direct determination of the positions of the deuterium atoms of the bound water in concanavalin A by neutron Laue crystallography [J].

Habash, J ;

Raftery, J ;

Nuttall, R ;

Price, HJ ;

Wilkinson, C ;

Kalb, AJ ;

Helliwell, JR .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2000, 56 :541-550

← 1 2 3 4 5 6 7 8 9 10 →