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Human SIRT3 bound to p53-AMC peptide 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 1.95 37.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.452 α = 90 b = 52.901 β = 92.52 c = 68.753 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 1.48 68.69 97.9 0.997 11.9 3.4 40650
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 1.48 1.5 0.754
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 1.48 68.69 37737 2908 97.85 0.2276 0.22615 0.2127 0.24628 0.231 RANDOM 22.63
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] 0.02 -0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.658 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_1_deg 6.344 r_long_range_B_refined 5.324 r_long_range_B_other 5.323 r_scangle_other 4.313 r_mcangle_other 2.913 r_mcangle_it 2.911 r_scbond_it 2.869 r_scbond_other 2.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.658 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_1_deg 6.344 r_long_range_B_refined 5.324 r_long_range_B_other 5.323 r_scangle_other 4.313 r_mcangle_other 2.913 r_mcangle_it 2.911 r_scbond_it 2.869 r_scbond_other 2.868 r_mcbond_it 2.023 r_mcbond_other 2.02 r_angle_refined_deg 1.8 r_angle_other_deg 0.626 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 2162 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction