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Human Sirt6 in complex with small molecule UBCS40
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MF6
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 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.364 α = 90 b = 91.364 β = 90 c = 144.212 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 2016-06-28 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) 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 48.07 99.7 0.161 12.89 11.4 39828 2.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.22 98 1.095 11.6
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 5MF6 2.1 45.68 37793 2032 99.74 0.16933 0.16726 0.1489 0.20806 0.1884 RANDOM 39.104
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] -11.91 -11.91 23.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.692 r_dihedral_angle_4_deg 19.866 r_dihedral_angle_3_deg 15.787 r_long_range_B_refined 8.801 r_long_range_B_other 8.8 r_dihedral_angle_1_deg 7.249 r_scangle_other 6.899 r_mcangle_it 5.422 r_mcangle_other 5.421 r_scbond_it 4.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.692 r_dihedral_angle_4_deg 19.866 r_dihedral_angle_3_deg 15.787 r_long_range_B_refined 8.801 r_long_range_B_other 8.8 r_dihedral_angle_1_deg 7.249 r_scangle_other 6.899 r_mcangle_it 5.422 r_mcangle_other 5.421 r_scbond_it 4.925 r_scbond_other 4.924 r_mcbond_other 4.054 r_mcbond_it 4.053 r_angle_refined_deg 2.447 r_angle_other_deg 1.274 r_chiral_restr 0.14 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 4337 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing