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Human Sirt6 in complex with the inhibitor S6020 and 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 5.7 293 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.359 α = 90 b = 91.359 β = 90 c = 142.962 γ = 120
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 2018-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.9184 BESSY 14.3
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 1.88 47.65 99.7 0.16 0.995 7.56 5.5 109024 38.737
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 1.88 1.99 2.81 0.365 0.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.88 45.68 54044 1073 99.84 0.19382 0.19319 0.1966 0.22691 0.2269 RANDOM 39.452
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] -18.37 -18.37 36.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 19.303 r_dihedral_angle_3_deg 14.993 r_long_range_B_refined 6.811 r_long_range_B_other 6.81 r_dihedral_angle_1_deg 6.682 r_scangle_other 5.001 r_mcangle_it 4.127 r_mcangle_other 4.126 r_scbond_it 3.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 19.303 r_dihedral_angle_3_deg 14.993 r_long_range_B_refined 6.811 r_long_range_B_other 6.81 r_dihedral_angle_1_deg 6.682 r_scangle_other 5.001 r_mcangle_it 4.127 r_mcangle_other 4.126 r_scbond_it 3.458 r_scbond_other 3.457 r_mcbond_it 3.055 r_mcbond_other 3.055 r_angle_other_deg 2.274 r_angle_refined_deg 1.577 r_chiral_restr 0.077 r_bond_other_d 0.034 r_gen_planes_other 0.012 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 4360 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing