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Human Sirt6 in complex with ADP-ribose and the activator cyanidin
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 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.387 α = 90 b = 91.387 β = 90 c = 143.806 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 2.1 47.94 99.9 0.16 0.998 11 11.3 39771 1.3 47.58
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 2.1 2.22 99.5 1.84 0.634 1.3 11.3
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 45.69 37769 2001 99.9 0.16517 0.16328 0.1681 0.19964 0.192 RANDOM 50.493
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] -20.23 -20.23 40.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.865 r_dihedral_angle_4_deg 20.735 r_dihedral_angle_3_deg 15.81 r_long_range_B_refined 11.226 r_long_range_B_other 11.225 r_scangle_other 8.388 r_dihedral_angle_1_deg 7.46 r_mcangle_it 6.545 r_mcangle_other 6.544 r_scbond_it 6.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.865 r_dihedral_angle_4_deg 20.735 r_dihedral_angle_3_deg 15.81 r_long_range_B_refined 11.226 r_long_range_B_other 11.225 r_scangle_other 8.388 r_dihedral_angle_1_deg 7.46 r_mcangle_it 6.545 r_mcangle_other 6.544 r_scbond_it 6.374 r_scbond_other 6.373 r_mcbond_other 5.498 r_mcbond_it 5.497 r_angle_other_deg 2.356 r_angle_refined_deg 1.95 r_chiral_restr 0.094 r_bond_other_d 0.034 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 4336 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 182
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing