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Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277.15 0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000
Crystal Properties Matthews coefficient Solvent content 4.29 71.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.506 α = 90 b = 193.506 β = 90 c = 49.869 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 PILATUS3 6M 2018-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9774 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.94891558608 48.38 99.7 0.097 0.997 7.91 3.4 43944 76.8711214453
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.05 0.733 0.782 1.34 3.3
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 MOLECULAR REPLACEMENT FREE R-VALUE 5YX2 2.94891558608 48.3765 1.96341412436 43857 1977 99.6500874781 0.216714672433 0.215787357675 0.2181 0.236316819954 0.2408 99.2882784718
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 24.2349447984 f_angle_d 0.685410366791 f_chiral_restr 0.0423126746298 f_plane_restr 0.00477652808252 f_bond_d 0.00356740280422
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7324 Nucleic Acid Atoms 1020 Solvent Atoms 11 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing