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 …

A brief history of macromolecular crystallography, illustrated by a family tree and its N obel fruits

M Jaskolski, Z Dauter, A Wlodawer - The FEBS journal, 2014 - Wiley Online Library
As a contribution to the celebration of the year 2014, declared by the United Nations to be
'The International Year of Crystallography', the FEBS Journal is dedicating this issue to …

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA, and Z-DNA

M Krepl, M Zgarbová, P Stadlbauer… - Journal of chemical …, 2012 - ACS Publications
Refinement of empirical force fields for nucleic acids requires their extensive testing using as
wide range of systems as possible. However, finding unambiguous reference data is not …

Mg2+ ions: do they bind to nucleobase nitrogens?

F Leonarski, L d'Ascenzo, P Auffinger - Nucleic acids research, 2017 - academic.oup.com
Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately
determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere …

Polarizable force field for DNA based on the classical Drude oscillator: II. Microsecond molecular dynamics simulations of duplex DNA

JA Lemkul, AD MacKerell Jr - Journal of chemical theory and …, 2017 - ACS Publications
The structure and dynamics of DNA are governed by a sensitive balance between base
stacking and pairing, hydration, and interactions with ions. Force-field models that include …

Stereochemistry and validation of macromolecular structures

A Wlodawer - Protein Crystallography: Methods and Protocols, 2017 - Springer
Macromolecular structure is governed by the strict rules of stereochemistry. Several
approaches to the validation of the correctness of the interpretation of crystallographic and …

Lone pair… π contacts and structure signatures of r (UNCG) tetraloops, Z-turns, and Z-steps: a WebFR3D survey

CL Zirbel, P Auffinger - Molecules, 2022 - mdpi.com
Z-DNA and Z-RNA have long appeared as oddities to nucleic acid scientists. However, their
Z-step constituents are recurrently observed in all types of nucleic acid systems including …

Cryo neutron crystallography demonstrates influence of RNA 2′-OH orientation on conformation, sugar pucker and water structure

JM Harp, TP Lybrand, PS Pallan, L Coates… - Nucleic acids …, 2022 - academic.oup.com
The ribose 2′-hydroxyl is the key chemical difference between RNA and DNA and primary
source of their divergent structural and functional characteristics. Macromolecular X-ray …

ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell

M Kowiel, M Jaskolski, Z Dauter - Acta Crystallographica Section D …, 2014 - journals.iucr.org
Despite the existence of numerous useful conventions in structural crystallography, for
example for the choice of the asymmetric part of the unit cell or of reciprocal space …

[PDF][PDF] Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining

Z Dauter, A Wlodawer, W Minor, M Jaskolski, B Rupp - IUCrJ, 2014 - journals.iucr.org
Whereas the vast majority of the more than 85 000 crystal structures of macromolecules
currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of …