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Crystal Structure of Human SIRT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.371 α = 90 b = 143.935 β = 117.1 c = 91.657 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 CCD ADSC QUANTUM 315 2008-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.7 65 85 0.121 9.9 3.9 45823 2
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) 2.7 2.85 87.6 0.417 4.5 3.8 6877
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 3GLR 2.7 65 43482 2313 84.69 0.18529 0.18218 0.1831 0.24376 0.2451 RANDOM 27.317
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] -1.98 -1.16 -0.31 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.458 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 17.005 r_dihedral_angle_1_deg 6.861 r_scangle_it 3.525 r_scbond_it 2.304 r_angle_refined_deg 1.452 r_mcangle_it 1.429 r_mcbond_it 1.012 r_nbtor_refined 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.458 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 17.005 r_dihedral_angle_1_deg 6.861 r_scangle_it 3.525 r_scbond_it 2.304 r_angle_refined_deg 1.452 r_mcangle_it 1.429 r_mcbond_it 1.012 r_nbtor_refined 0.339 r_symmetry_vdw_refined 0.304 r_nbd_refined 0.287 r_xyhbond_nbd_refined 0.198 r_symmetry_hbond_refined 0.18 r_chiral_restr 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12860 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 25
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling