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Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies

Elke De Zitter, Nicolas Coquelle, Paula Oeser, Thomas R. M. Barends, Jacques‐Philippe Colletier

2022Communications Biology57 citationsDOIOpen Access PDF

Abstract

Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, which hinders structure determination by conventional methods. To automatically extract structural information pertaining to these states, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of methods hitherto not available; (iii) calculates extrapolated structure factors using the various proposed formalisms while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures in real and reciprocal-space. The use of Xtrapol8 could accelerate data processing in kinetic and time-resolved crystallographic studies, and as well foster the identification of drug-targetable states in ligand-based crystallography.

Topics & Concepts

WeightingOccupancyRotation formalisms in three dimensionsBayesian probabilityLigand (biochemistry)CrystallographyReciprocal latticeComputer scienceChemistryData miningComputational chemistryStatistical physicsAlgorithmMathematicsPhysicsArtificial intelligenceEngineeringQuantum mechanicsDiffractionAcousticsBiochemistryArchitectural engineeringGeometryReceptorComputational Drug Discovery MethodsProtein Structure and DynamicsEnzyme Structure and Function
Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies | Litcius