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Crystal structure of human Sirt2 in complex with a TNFa-Myr analogue TNFn-34
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 19 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.106 α = 90 b = 73.339 β = 95.17 c = 55.229 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 16M 2023-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9188 SLS X06SA
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 1.65 44 99.9 0.084 0.091 0.035 0.998 12.9 6.7 34505
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 1.65 1.68 0.837 0.904 0.339 0.804 2.6 7
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 1.65 44 1.34 34478 1744 99.81 0.1868 0.1855 0.185 0.2121 0.2116
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 7.04 f_angle_d 1.059 f_chiral_restr 0.063 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2373 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing