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Human SIRT3 bound to p53-AMC peptide, Carba-NAD, and Honokiol
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 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.683 α = 90 b = 159.432 β = 90.61 c = 53.047 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 APS BEAMLINE 19-BM 0.9786 APS 19-BM
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 2.4 44.16 96.2 0.983 10.4 3.1 21620
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 2.4 2.44 0.807
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 2.4 44.16 20550 1038 95.95 0.19947 0.19442 0.2017 0.30262 0.3046 RANDOM 56.789
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] 0.43 0.12 -0.15 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.072 r_dihedral_angle_3_deg 18.943 r_long_range_B_other 18.663 r_long_range_B_refined 18.661 r_scangle_other 15.754 r_mcangle_other 12.833 r_mcangle_it 12.832 r_scbond_it 11.318 r_scbond_other 11.316 r_mcbond_other 9.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.072 r_dihedral_angle_3_deg 18.943 r_long_range_B_other 18.663 r_long_range_B_refined 18.661 r_scangle_other 15.754 r_mcangle_other 12.833 r_mcangle_it 12.832 r_scbond_it 11.318 r_scbond_other 11.316 r_mcbond_other 9.939 r_mcbond_it 9.938 r_dihedral_angle_1_deg 9.779 r_angle_refined_deg 2.914 r_angle_other_deg 0.957 r_chiral_restr 0.131 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4286 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction