Computational protocol: Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly

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Protocol publication

[…] Diffraction data for the ΔN90-PGAM5 and ΔN54-PGAM5 crystals were collected on in-house Rigaku FRE-Superbright and Diamond Light Source, respectively. Data were processed with MOSFLM () and subsequent scaled with SCALA (). Initial apo structure was solved by SIRAS using the program SHELXD () and SHARP (). The improve phases obtained after solvent flattening were used for automated model building with Buccaneer (). Structure solution of both phosphate complexes were achieved by molecular replacement with the program PHASER () and the apo-structure as a model. Both PGAM5 structures were subjected to iterative cycles of manual building alternated with refinement using COOT () and REFMAC (), respectively. TLS definitions were determined by the TLSMD server, and used in the final refinement step. Geometric correctness of both structures was verified by MOLPROBITY (). Data collection and refinement statistics are summarised in . […]

Pipeline specifications

Software tools iMosflm, CCP4, SHELX, Buccaneer, Coot, MolProbity
Applications Small-angle scattering, Protein structure analysis
Chemicals Hydrogen