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Human Sirt6 13-308 in complex with ADP-ribose and the activator MDL-801
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 5.7 293 100 mM Bis-Tris pH 5.7, 1.6 M (NH4)2SO4, and 10% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.61 52.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.175 α = 90 b = 91.175 β = 90 c = 143.584 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 2019-09-26 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 1.95 47.86 99.9 0.16 0.997 11.3 11.5 49197 38.68
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 1.95 2.07 99.4 1.61 0.546 1.7 11.4
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 3K35 1.95 45.59 47072 2124 99.88 0.1502 0.1496 0.1547 0.1645 0.17 RANDOM 37.461
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] -10.52 -10.52 21.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 21.957 r_dihedral_angle_3_deg 16.169 r_dihedral_angle_1_deg 7.119 r_angle_other_deg 2.375 r_angle_refined_deg 2.121 r_chiral_restr 0.113 r_bond_other_d 0.034 r_gen_planes_other 0.022 r_bond_refined_d 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 21.957 r_dihedral_angle_3_deg 16.169 r_dihedral_angle_1_deg 7.119 r_angle_other_deg 2.375 r_angle_refined_deg 2.121 r_chiral_restr 0.113 r_bond_other_d 0.034 r_gen_planes_other 0.022 r_bond_refined_d 0.017 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4360 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PDB_EXTRACT data extraction