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Human Sirt6 3-318 in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.689 α = 90 b = 136.31 β = 117.37 c = 90.096 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 6M 2019-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.75 46.72 99 0.14 0.994 6.3 3.9 191591
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.86 97.7 1.59 0.342 0.8 3.6
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 3K35 1.75 46.72 189464 2099 99.14 0.2006 0.2003 0.2074 0.2246 0.229 RANDOM 31.337
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] -1.11 -0.21 1.12 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.101 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_3_deg 12.966 r_dihedral_angle_1_deg 6.337 r_angle_other_deg 2.254 r_angle_refined_deg 1.525 r_chiral_restr 0.074 r_bond_other_d 0.034 r_gen_planes_other 0.012 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.101 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_3_deg 12.966 r_dihedral_angle_1_deg 6.337 r_angle_other_deg 2.254 r_angle_refined_deg 1.525 r_chiral_restr 0.074 r_bond_other_d 0.034 r_gen_planes_other 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13200 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 434
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PDB_EXTRACT data extraction