The Phenix software for automated determination of macromolecular structures

PD Adams, PV Afonine, G Bunkóczi, VB Chen… - Methods, 2011 - Elsevier
X-ray crystallography is a critical tool in the study of biological systems. It is able to provide
information that has been a prerequisite to understanding the fundamentals of life. It is also a …

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

A Wlodawer, W Minor, Z Dauter… - The FEBS journal, 2013 - Wiley Online Library
The number of macromolecular structures deposited in the Protein Data Bank now
approaches 100 000, with the vast majority of them determined by crystallographic methods …

[PDF][PDF] The PDB_REDO server for macromolecular structure model optimization

RP Joosten, F Long, GN Murshudov, A Perrakis - IUCrJ, 2014 - journals.iucr.org
The refinement and validation of a crystallographic structure model is the last step before the
coordinates and the associated data are submitted to the Protein Data Bank (PDB). The …

[HTML][HTML] MINDY-1 is a member of an evolutionarily conserved and structurally distinct new family of deubiquitinating enzymes

SAA Rehman, YA Kristariyanto, SY Choi, PJ Nkosi… - Molecular cell, 2016 - cell.com
Deubiquitinating enzymes (DUBs) remove ubiquitin (Ub) from Ub-conjugated substrates to
regulate the functional outcome of ubiquitylation. Here we report the discovery of a new …

[PDF][PDF] Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

GM Sheldrick - Acta Crystallographica Section D: Biological …, 2010 - journals.iucr.org
The programs SHELXC, SHELXD and SHELXE are designed to provide simple, robust and
efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP …

[PDF][PDF] HKL-3000: the integration of data reduction and structure solution–from diffraction images to an initial model in minutes

W Minor, M Cymborowski, Z Otwinowski… - … section D: biological …, 2006 - journals.iucr.org
A new approach that integrates data collection, data reduction, phasing and model building
significantly accelerates the process of structure determination and on average minimizes …

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

G Langer, SX Cohen, VS Lamzin, A Perrakis - Nature protocols, 2008 - nature.com
ARP/wARP is a software suite to build macromolecular models in X-ray crystallography
electron density maps. Structural genomics initiatives and the study of complex …

Discovery and characterization of ZUFSP/ZUP1, a distinct deubiquitinase class important for genome stability

D Kwasna, SAA Rehman, J Natarajan, S Matthews… - Molecular Cell, 2018 - cell.com
Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we
report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal …

IL MILIONE: a suite of computer programs for crystal structure solution of proteins

MC Burla, R Caliandro, M Camalli… - Journal of Applied …, 2007 - journals.iucr.org
IL MILIONEIl Milione is the title of the book by Marco Polo, dictated to Rustichello da Pisa in
1298 in the Genova prison where Marco was imprisoned after a naval battle between …

[PDF][PDF] BALBES: a molecular-replacement pipeline

F Long, AA Vagin, P Young… - … Section D: Biological …, 2008 - journals.iucr.org
The number of macromolecular structures solved and deposited in the Protein Data Bank
(PDB) is higher than 40 000. Using this information in macromolecular crystallography (MX) …