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Human SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).
Crystal Properties Matthews coefficient Solvent content 2.13 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.339 α = 90 b = 53.178 β = 91.75 c = 68.539 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 PILATUS 6M 2021-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 ALBA XALOC
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 1.74 42.04 99.1 0.993 7.4 4.2 25473
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 1.74 1.77 0.649
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.74 42.04 24207 1259 99.06 0.24383 0.24186 0.2396 0.28155 0.2809 RANDOM 26.339
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] -1.2 0.19 -0.56 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.412 r_dihedral_angle_3_deg 16.375 r_dihedral_angle_4_deg 16.286 r_dihedral_angle_1_deg 7.872 r_long_range_B_refined 5.675 r_mcangle_it 2.836 r_scbond_it 2.546 r_mcbond_it 1.988 r_angle_refined_deg 0.806 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.412 r_dihedral_angle_3_deg 16.375 r_dihedral_angle_4_deg 16.286 r_dihedral_angle_1_deg 7.872 r_long_range_B_refined 5.675 r_mcangle_it 2.836 r_scbond_it 2.546 r_mcbond_it 1.988 r_angle_refined_deg 0.806 r_chiral_restr 0.066 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2070 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing XDS data processing