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Crystal structure of human SIRT3 in complex with compound (2-butylbenzofuran-3-yl)(4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl)methanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GLS
Crystallization Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.317 α = 90 b = 116.317 β = 90 c = 45.655 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2013-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979220 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 2 100.73 0.094 15.1 6 24073
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 2.05 0.427 4.2 6
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 3GLS 2 100.73 22590 1216 98.57 0.16928 0.16737 0.1785 0.20373 0.2168 RANDOM 32.239
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] 0.08 0.04 0.08 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.313 r_dihedral_angle_4_deg 17.17 r_long_range_B_other 15.697 r_long_range_B_refined 15.584 r_dihedral_angle_3_deg 14.089 r_scangle_other 8.411 r_dihedral_angle_1_deg 6.284 r_scbond_other 5.665 r_mcangle_it 4.034 r_scbond_it 4.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.313 r_dihedral_angle_4_deg 17.17 r_long_range_B_other 15.697 r_long_range_B_refined 15.584 r_dihedral_angle_3_deg 14.089 r_scangle_other 8.411 r_dihedral_angle_1_deg 6.284 r_scbond_other 5.665 r_mcangle_it 4.034 r_scbond_it 4.034 r_mcangle_other 4.031 r_mcbond_it 2.901 r_mcbond_other 2.901 r_angle_refined_deg 1.943 r_angle_other_deg 1.048 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 2133 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling