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Human Sirt6 in complex with activator UBCS38
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 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.868 α = 90 b = 91.868 β = 90 c = 145.353 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 2.07 48.45 99.8 0.203 8.73 11.3 42356 2.3
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 2.07 2.19 99 1.103 11.5
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 2.07 45.93 40233 2121 99.82 0.14604 0.1437 0.1483 0.19175 0.192 RANDOM 31.893
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] -9.79 -9.79 19.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.91 r_dihedral_angle_4_deg 21.32 r_dihedral_angle_3_deg 16.285 r_long_range_B_refined 7.407 r_long_range_B_other 7.407 r_dihedral_angle_1_deg 6.659 r_scangle_other 5.689 r_mcangle_it 4.451 r_mcangle_other 4.451 r_scbond_it 4.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.91 r_dihedral_angle_4_deg 21.32 r_dihedral_angle_3_deg 16.285 r_long_range_B_refined 7.407 r_long_range_B_other 7.407 r_dihedral_angle_1_deg 6.659 r_scangle_other 5.689 r_mcangle_it 4.451 r_mcangle_other 4.451 r_scbond_it 4.101 r_scbond_other 4.073 r_angle_other_deg 3.741 r_mcbond_it 3.326 r_mcbond_other 3.325 r_angle_refined_deg 2.41 r_chiral_restr 0.227 r_bond_refined_d 0.024 r_gen_planes_other 0.02 r_gen_planes_refined 0.012 r_bond_other_d 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 4309 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing