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Human Sirt6 in complex with ADP-ribose and fragment 4-nitrocatechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MF6 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 2.61 52.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.974 α = 90 b = 90.974 β = 90 c = 144.316 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 2M 2017-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 2.13 48.11 99.8 0.24 0.993 6.89 6.8 37821 45.264
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 2.13 2.26 98.7 2.6 0.31 0.67 6.4
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 2.13 41.06 35961 1859 99.77 0.2136 0.2112 0.2117 0.2608 0.2467 RANDOM 51.57
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] -27.86 -27.86 55.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.085 r_dihedral_angle_3_deg 15.37 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_1_deg 6.472 r_angle_refined_deg 1.302 r_angle_other_deg 1.166 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.085 r_dihedral_angle_3_deg 15.37 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_1_deg 6.472 r_angle_refined_deg 1.302 r_angle_other_deg 1.166 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4360 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction