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Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 292 14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Crystal Properties Matthews coefficient Solvent content 2.79 55.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.598 α = 90 b = 77.416 β = 125.762 c = 116.514 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2018-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.09 41.81 96.4 0.109 0.066 12 3.5 130375 38.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.16 89 1.106 0.817 0.298 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 6X9J 2.09 41.81 1.35 130103 3877 96.08 0.186 0.185 0.1858 0.2159 0.2171 60.91
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 f_dihedral_angle_d 19.0655 f_angle_d 0.7316 f_chiral_restr 0.0464 f_plane_restr 0.007 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6414 Nucleic Acid Atoms 487 Solvent Atoms 251 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing