Computational protocol: Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues

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Protocol publication

[…] The CCP4 package of programs [], specifically SCALEPACK2MTZ, ctruncate, MTZDUMP, Unique, CAD, FREERFLAG and MTZUTILS, were used to convert intensities into structure factors and 5% of the reflections was flagged for Rfree calculations. The structure of TfAA10A was solved using SIRAS with Crank2 [, ]. Buccaneer [] was used to auto build the resulting partial model. Refinement and manual correction were performed using REFMAC5 [] version 5.7.0029 and Coot [] version 0.6.2. Phenix.refine version 1.10-2155 [] was used for occupancy refinement followed by REFMAC5. The MOLPROBITY method [] was used to analyze the Ramachandran plot and root mean square deviations (rmsd) of bond lengths and angles were calculated from ideal values of Engh and Huber stereochemical parameters []. Wilson B-factor was calculated using CTRUNCATE version 1.17.7. The data collection and refinement statistics are shown in TableĀ . [...] Programs Coot and PyMOL (http://www.pymol.org) were used for comparing and analyzing structures. This structure has been deposited to the protein data bank (PDB; www.rcsb.org) with entry code 5UIZ. […]

Pipeline specifications

Software tools CCP4, Crank, Buccaneer, REFMAC5, Coot, PHENIX, MolProbity, PyMOL
Application Protein structure analysis
Organisms Thermobifida fusca, Dipturus trachyderma
Chemicals Copper