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Structure of human SIRT3 in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FVT PDB ENTRY 4FVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 30% (V/V) PEG600, 5%(W/V) PEG1000, 10% (V/V) GLYCEROL, 0.1 M MES, PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.54 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.9 α = 90 b = 66.67 β = 90 c = 66.85 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH DYNAMICALLY BENDABLE MIRROR 2012-11-14 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 1.3 25 98.4 0.09 15.1 6.8 69702
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 1.3 1.4 96.8 1.36 1.2 4.1
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 4FVT 1.3 47.21 66216 3485 98.37 0.13993 0.13781 0.1378 0.1795 0.1796 RANDOM 20.476
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] -0.91 -0.03 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_sphericity_free 31.321 r_dihedral_angle_4_deg 20.217 r_dihedral_angle_3_deg 11.835 r_sphericity_bonded 11.667 r_dihedral_angle_1_deg 6.17 r_rigid_bond_restr 6.036 r_angle_refined_deg 2.192 r_angle_other_deg 1.249 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_sphericity_free 31.321 r_dihedral_angle_4_deg 20.217 r_dihedral_angle_3_deg 11.835 r_sphericity_bonded 11.667 r_dihedral_angle_1_deg 6.17 r_rigid_bond_restr 6.036 r_angle_refined_deg 2.192 r_angle_other_deg 1.249 r_chiral_restr 0.139 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_bond_other_d 0.004 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_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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2124 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing