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Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801
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 2.38 48.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.51 α = 90 b = 136.534 β = 117.71 c = 89.873 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 PILATUS3 2M 2019-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 2.1 46.39 99.4 0.13 0.999 15.7 14 110958 51.46
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 2.1 2.23 97.6 2.4 0.499 1.1 14.3
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 2.1 46.39 108840 2101 99.6 0.2049 0.2044 0.2117 0.2298 0.2322 RANDOM 53.293
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] -2.55 -0.48 1.69 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.398 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_1_deg 6.185 r_angle_refined_deg 1.484 r_angle_other_deg 1.322 r_chiral_restr 0.069 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.398 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_1_deg 6.185 r_angle_refined_deg 1.484 r_angle_other_deg 1.322 r_chiral_restr 0.069 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12939 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 539
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PDB_EXTRACT data extraction