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Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-5 and NAD+
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 24 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.357 α = 90 b = 74.466 β = 97.3 c = 56.211 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 4M 2023-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.55 55.75 98.9 0.066 0.071 0.027 0.997 15.8 7.1 44955
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 1.55 1.58 0.608 0.655 0.243 0.879 3.4 7.2
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 1.55 44.63 1.35 44927 2160 98.81 0.1783 0.1771 0.1773 0.2009 0.2001
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 7.442 f_angle_d 0.911 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 2408 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement Aimless data scaling autoPROC data reduction PHASER phasing