Citations
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Journal ArticleDOI
A short history of SHELX
TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Crystal structure refinement with SHELXL
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Journal ArticleDOI
Coot: model-building tools for molecular graphics.
Paul Emsley,Kevin Cowtan +1 more
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
References
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Journal ArticleDOI
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source
Scott Classen,Greg L. Hura,James M. Holton,James M. Holton,Robert P. Rambo,Ivan Rodic,Patrick McGuire,Kevin Dyer,Michal Hammel,George Meigs,Kenneth A. Frankel,John A. Tainer +11 more
TL;DR: The SIBYLS beamline of the Advanced Light Source is a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline and key features and capabilities are described along with implementation and performance.
Journal ArticleDOI
PDB_REDO: constructive validation, more than just looking for errors
TL;DR: The decision-making algorithms and software used in PDB_REDO to re-refine and rebuild crystallographic protein structures in the PDB are presented and discussed.
Journal ArticleDOI
Room-temperature macromolecular serial crystallography using synchrotron radiation.
Francesco Stellato,Dominik Oberthür,Mengning Liang,Richard Bean,Cornelius Gati,Oleksandr Yefanov,Anton Barty,Anja Burkhardt,Pontus Fischer,Lorenzo Galli,Richard A. Kirian,Jan Meyer,Saravanan Panneerselvam,Chun Hong Yoon,Fedor Chervinskii,Emily M. Speller,Thomas A. White,Christian Betzel,Alke Meents,Henry N. Chapman +19 more
TL;DR: The room-temperature structure of lysozyme is determined using 40000 individual diffraction patterns from micro-crystals flowing in liquid suspension across a synchrotron microfocus beamline.
Journal ArticleDOI
Entrapment of Carbon Dioxide in the Active Site of Carbonic Anhydrase II
John F. Domsic,Balendu Sankara Avvaru,Chae Un Kim,Sol M. Gruner,Mavis Agbandje-McKenna,David N. Silverman,Robert McKenna +6 more
TL;DR: Using CO2-pressurized, cryo-cooled crystals to capture the first step of CO2 hydration catalyzed by the zinc-metalloenzyme human carbonic anhydrase II, the binding of substrate CO2, for both the holo and the apo (without zinc) enzyme to 1.1Å resolution is shown.
Journal ArticleDOI
PDB_REDO : automated re-refinement of X-ray structure models in the PDB
Robbie P. Joosten,Jean Salzemann,V. Bloch,Heinz Stockinger,A.-C. Berglund,C. Blanchet,Erik Bongcam-Rudloff,Christophe Combet,A.L. Da Costa,Gilbert Deléage,M. Diarena,Roberto Fabbretti,G. Fettahi,Volker Flegel,Andreas Gisel,Vinod Kasam,T. Kervinen,Eija Korpelainen,K. Mattila,Marco Pagni,Matthieu Reichstadt,Vincent Breton,Ian J. Tickle,Gert Vriend +23 more
TL;DR: The majority of previously deposited X-ray structures can be improved by applying current refinement methods, and these methods can be applied to improve the structure itself.