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Human Sirt6 in complex with ADP-ribose and the inhibitor catechin gallate
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 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.917 α = 90 b = 91.917 β = 90 c = 144.368 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 14.1 0.918 BESSY 14.1
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 2.01 48.12 98.9 0.16 0.996 9.7 10.1 45089 1.3 38.92
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 2.01 2.14 96.2 1.9 0.71 1.3 8.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5MF6 2.01 45.96 42989 2099 98.88 0.16474 0.16311 0.19853 0.2055 RANDOM 38.796
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] -22.25 -22.25 44.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.146 r_dihedral_angle_4_deg 18.56 r_dihedral_angle_3_deg 15.69 r_long_range_B_other 9.11 r_long_range_B_refined 9.107 r_dihedral_angle_1_deg 8.312 r_scangle_other 7.027 r_mcangle_it 6.157 r_mcangle_other 6.156 r_scbond_it 5.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.146 r_dihedral_angle_4_deg 18.56 r_dihedral_angle_3_deg 15.69 r_long_range_B_other 9.11 r_long_range_B_refined 9.107 r_dihedral_angle_1_deg 8.312 r_scangle_other 7.027 r_mcangle_it 6.157 r_mcangle_other 6.156 r_scbond_it 5.476 r_scbond_other 5.475 r_mcbond_other 4.888 r_mcbond_it 4.887 r_angle_refined_deg 2.281 r_angle_other_deg 1.427 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.003 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 4350 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing