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Discovery of a compound that activates SIRT3 to deacetylate Manganese Superoxide Dismutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SZX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1.5M potassium phosphate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.12 α = 90 b = 80.12 β = 90 c = 242.87 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 52.74 99.6 0.11 17.8 16.1 21413
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 100 0.22 10.9 17.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1SZX 2.3 52.74 20241 1095 99.48 0.21498 0.21308 0.2149 0.24975 0.2503 RANDOM 31.362
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] 0.07 0.07 0.07 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.854 r_dihedral_angle_3_deg 16.299 r_dihedral_angle_4_deg 15.227 r_long_range_B_refined 6.01 r_long_range_B_other 6.008 r_dihedral_angle_1_deg 5.296 r_scangle_other 4.453 r_mcangle_it 3.266 r_mcangle_other 3.266 r_scbond_it 2.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.854 r_dihedral_angle_3_deg 16.299 r_dihedral_angle_4_deg 15.227 r_long_range_B_refined 6.01 r_long_range_B_other 6.008 r_dihedral_angle_1_deg 5.296 r_scangle_other 4.453 r_mcangle_it 3.266 r_mcangle_other 3.266 r_scbond_it 2.945 r_scbond_other 2.944 r_mcbond_it 2.304 r_mcbond_other 2.298 r_angle_refined_deg 1.297 r_angle_other_deg 0.866 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.005 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 3090 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 2
Software Software Software Name Purpose iMOSFLM data processing SCALA data scaling PHASER phasing Coot model building REFMAC refinement