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Crystal structure of human SIRT6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 0.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 4.4 72.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.795 α = 90 b = 161.795 β = 90 c = 161.795 γ = 90
Symmetry Space Group P 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2019-01-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0000 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.53 114.41 100 0.995 24 22.4 24693
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.62 0.836
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 5X16 2.53 114.41 23434 1251 99.97 0.2085 0.2064 0.2135 0.2479 0.2538 RANDOM 45.614
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 16.024 r_dihedral_angle_1_deg 7.017 r_angle_refined_deg 2.075 r_angle_other_deg 1.124 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 16.024 r_dihedral_angle_1_deg 7.017 r_angle_refined_deg 2.075 r_angle_other_deg 1.124 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2337 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building SCALEPACK data scaling PHASER phasing