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Crystal structure of human Sirt3 in complex with an acetylated HIV1 Tat-46-54 substrate peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM MES, pH 6.0, 30% (w/v) PEG 200, 5% (w/v) PEG 3000 as reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.99 58.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.721 α = 90 b = 127.76 β = 90 c = 77.576 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M 2018-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 39.36 99.89 0.999 13.93 11.2 47332 31.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.709 99.94 0.469 0.89 11.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4FVT 1.65 39.36 1.33 47317 1090 99.79 0.1813 0.1807 0.1829 0.2089 0.2116 36.94
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 20.3968 f_angle_d 1.382 f_chiral_restr 0.0963 f_bond_d 0.0166 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2233 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction PHASER phasing Coot model building PHENIX refinement XDS data scaling