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Pipeline publication

[…]  M Hepes buffer, pH 7.5. Rod shape crystals grew in about 6 days to their maximum size of 0.2−0.3 mm × 0.1−0.2 mm., X-ray diffraction data for SIRT2/BHJH-TM1 were collected at Beamline A1 at the Cornell High Energy Synchrotron Source (CHESS) using an ADSC Quantum 210 CCD detector. The data collection temperature was 100 K. A total of 180° of data was collected with an oscillation range of 1° per frame and an exposure time of 5 s per frame. X-ray diffraction data were indexed, integrated, scaled, and merged using the program HKL2000 to 2.1 Å resolution. Data collection and processing statistics are summarized in ., The structure of SIRT2/BHJH-TM1 was determined by molecular replacement using Phaser as implemented in the CCP4 program package. A monomer of human SIRT2 Apo-form (PDB ID: 3ZGO) was used as the search model. The initial model was refined to an R-factor of 28.74% and R-free of 37.71% by using the maximum likelihood method implemented in REFMAC5 as part of CCP4 program suite and was manually adjusted using COOT. After several cycles of refinement and model building, BHJH-TM1 and water molecules were added. The final model was refined to an R-factor of 22.1% and R-free of 27.3%. The Ramachandran plot shows 91.7% of residues in the most favorable regions, 8.1% in the allowed regions and 0.2% in generously allowed regions. No residue was in disallowed regions. Refinement statistics are summarized in ., Atomic coordinates and structure factors for the reported crystal structure have been deposited with the Protein Data Bank under accession code 4R8M., This work was supported in part by NIH R01CA152870 (Q.H. and H.L.), HK-RGC C7037-14G and GRF766911 (Q.H.). The crystallographic data were collected […]

Pipeline specifications

Software tools CCP4, REFMAC5, Coot