Computational protocol: Large-Scale Structural Analysis of the Classical Human Protein Tyrosine Phosphatome

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Protocol publication

[…] Individual proteins were crystallized in sitting drops at either 4°C or 20°C. Crystals were cryoprotected and flash frozen, and X-ray diffraction data were collected at 100 K on beam lines X10SA at the Swiss Light Source (SLS), on beam line 14.1 at the Berliner Elektronenspeicherring-Gesellschaft für Synchrotronstrahlung (BESSY), and at a Rigaku FRE Superbright home source. Diffraction images were indexed and integrated using MOSFLM () or DENZO in HKL2000 () or XDS () and data were scaled using SCALA, SCALEPACK in HKL2000, or XSCALE, respectively. Structures were solved by molecular replacement using PHASER () and were refined against maximum likelihood targets using restrained refinement and TLS protocols implemented in REFMAC (). Iterative rounds of refinement were interspersed with manual rebuilding in COOT (). Additional information is compiled in the and is also available at http://www.sgc.ox.ac.uk/research/phosphatases. […]

Pipeline specifications

Software tools iMosflm, XDS, CCP4, Coot
Applications Small-angle scattering, Protein structure analysis
Organisms Homo sapiens