Computational protocol: Automated harvesting and processing of protein crystals through laser photoablation

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Protocol publication

[…] Diffraction data were collected on the BM14, ID14-EH4, ID29, ID23-EH1 or ID23-EH2 beamlines at the European Synchrotron Radiation Facility (ESRF; Grenoble, France). Crystallo­graphic data reduction and scaling was performed with the XDS software (Kabsch, 2010). Initial phases were obtained by the molecular-replacement method using MOLREP (Vagin & Teplyakov, 2010) and the following search models from the Protein Data Bank: PDB entries 1hcl (Schulze-Gahmen et al., 1996) for CDK2, 1ko9 (Bjørås et al., 2002) for OGG1, 4pvl (Haupt et al., 2014) for TTR, 4c9c (Casañal et al., 2013) for Fra a 2, 4uwg (Pasquier et al., 2015) for Vps34, 4b0d (Cipriani et al., 2012) for lysozyme, 2prk (Betzel et al., 1988) for proteinase K and 4axr (Cipriani et al., 2012) for thaumatin. Successive rounds of automatic refinement and manual building were carried out with REFMAC5 (Murshudov et al., 2011) and Coot (Emsley et al., 2010). Initial solvent models were established with ARP/wARP (Langer et al., 2008) and refined manually. MolProbity (Chen et al., 2010) was used to evaluate the general quality of the final models. Structure factors and atomic models for all of the structures discussed in this work have been deposited in the Protein Data Bank (PDB entries 5amz, 5amx, 5ebh, 5ano, 5anl, 5amw, 5an4, 5dwp, 5ank, 5anj, 5ani, 5ang, 5ane and 5and). […]

Pipeline specifications

Software tools XDS, Molrep, REFMAC5, Coot, ARP/wARP, MolProbity
Applications Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma