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Crystal structure of human SIRT2 in complex with SirReal-triazole inhibitor SH10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystals of the SIRT2-SH10 complex (18.0 mg/mL SIRT2, 10 mM NAD+, 1.67 mM of SH10 with 1.67 % (v/v) final DMSO concentration) formed after two days in wells of protein solution and reservoir solution containing 19 % (w/v) PEG 3350 in 0.1 M Bis-Tris at pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.92 α = 90 b = 77.165 β = 93.78 c = 55.817 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 77.17 99.9 0.065 0.071 0.027 0.999 13.8 6.8 47249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 0.969 1.049 0.397 0.78 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 55.7 1.34 47201 2372 99.84 0.1608 0.1597 0.1604 0.1821 0.1819
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.785 f_angle_d 0.877 f_chiral_restr 0.054 f_plane_restr 0.01 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement Aimless data scaling autoPROC data reduction PHASER phasing