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Improved complex structure of human Sirtuin 6 with its inhibitor cis-resveratrol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K35
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 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.276 α = 90 b = 91.276 β = 90 c = 143.23 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 2018-06-14 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) 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 1.75 47.74 99.9 0.12 0.999 12.9 10.2 67988 35.441
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 1.75 1.86 99.5 2.11 0.421 1.18
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.75 45.64 65918 2069 99.9 0.16725 0.1666 0.18761 0.1784 RANDOM 33.955
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] -9.14 -9.14 18.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.569 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 14.395 r_dihedral_angle_1_deg 6.833 r_long_range_B_refined 6.58 r_long_range_B_other 6.549 r_scangle_other 4.807 r_mcangle_other 3.931 r_mcangle_it 3.93 r_scbond_it 3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.569 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 14.395 r_dihedral_angle_1_deg 6.833 r_long_range_B_refined 6.58 r_long_range_B_other 6.549 r_scangle_other 4.807 r_mcangle_other 3.931 r_mcangle_it 3.93 r_scbond_it 3.38 r_scbond_other 3.343 r_mcbond_it 2.968 r_mcbond_other 2.967 r_angle_other_deg 2.294 r_angle_refined_deg 1.649 r_chiral_restr 0.08 r_bond_other_d 0.034 r_gen_planes_other 0.018 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 4364 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 197
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing