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Crystal structure of human Sirt3 at an improved resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M magnesium chloride, 25 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.99 α = 90 b = 143.85 β = 116.33 c = 89.46 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 PIXEL DECTRIS PILATUS 2M 2012-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 1.83 33.66 99.8 0.084 10 3.6 168813
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 1.83 1.86 0.815
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GLS 1.83 33.66 160291 8479 99.8 0.17635 0.17494 0.20316 0.1965 RANDOM 24.762
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] -0.02 -0.12 -0.09 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.949 r_dihedral_angle_4_deg 14.013 r_dihedral_angle_3_deg 13.105 r_dihedral_angle_1_deg 5.38 r_long_range_B_refined 5.369 r_long_range_B_other 5.201 r_scangle_other 2.427 r_mcangle_it 1.791 r_mcangle_other 1.791 r_scbond_it 1.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.949 r_dihedral_angle_4_deg 14.013 r_dihedral_angle_3_deg 13.105 r_dihedral_angle_1_deg 5.38 r_long_range_B_refined 5.369 r_long_range_B_other 5.201 r_scangle_other 2.427 r_mcangle_it 1.791 r_mcangle_other 1.791 r_scbond_it 1.454 r_scbond_other 1.454 r_angle_refined_deg 1.336 r_mcbond_it 1.063 r_mcbond_other 1.063 r_angle_other_deg 0.816 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 12775 Nucleic Acid Atoms Solvent Atoms 1257 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Aimless data scaling XDS data reduction