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Human SIRT6 in complex with inhibitor 7702
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M Bis-tris pH 5.7, 1.6 M (NH4)2SO4, 10% PEG400
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.318 α = 90 b = 91.318 β = 90 c = 143.674 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 EIGER2 S 16M 2022-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9792 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 40.97 99.9 0.99 15.35 19.17 34506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.279 0.965
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 2.2 40.97 32687 1735 99.96 0.19442 0.19223 0.204 0.23751 0.2374 RANDOM 47.79
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 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.109 r_dihedral_angle_4_deg 17.847 r_dihedral_angle_3_deg 15.455 r_long_range_B_other 11.043 r_long_range_B_refined 11.037 r_scangle_other 7.364 r_dihedral_angle_1_deg 7.04 r_mcangle_it 5.845 r_mcangle_other 5.845 r_scbond_it 5.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.109 r_dihedral_angle_4_deg 17.847 r_dihedral_angle_3_deg 15.455 r_long_range_B_other 11.043 r_long_range_B_refined 11.037 r_scangle_other 7.364 r_dihedral_angle_1_deg 7.04 r_mcangle_it 5.845 r_mcangle_other 5.845 r_scbond_it 5.215 r_scbond_other 5.18 r_mcbond_it 4.519 r_mcbond_other 4.517 r_angle_refined_deg 1.598 r_angle_other_deg 1.292 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 4392 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing