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Structure of human SIRT3 in complex with SRT1720 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GLS PDB ENTRY 3GLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
Crystal Properties Matthews coefficient Solvent content 4.41 72.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 227.82 α = 90 b = 246.06 β = 123.88 c = 127.34 γ = 90
Symmetry Space Group C 1 2 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 DYNAMICALLY BENDABLE MIRROR 2013-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 3.25 25 99.4 0.14 9.3 3.9 91158
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 3.25 3.3 99.6 1.44 1.1 3.9
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 PDB ENTRY 3GLS 3.25 48.57 86600 4558 99.82 0.21073 0.20791 0.2027 0.26534 0.2576 RANDOM 97.868
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] -0.87 -0.07 -3.78 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_3_deg 20.223 r_dihedral_angle_4_deg 19.362 r_dihedral_angle_1_deg 7.615 r_angle_refined_deg 2.22 r_angle_other_deg 1.164 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_3_deg 20.223 r_dihedral_angle_4_deg 19.362 r_dihedral_angle_1_deg 7.615 r_angle_refined_deg 2.22 r_angle_other_deg 1.164 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 25548 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 972
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing