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Crystal structure of DNMT3B(N779A)-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 4.04 69.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.506 α = 90 b = 191.506 β = 90 c = 49.597 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 CCD ADSC QUANTUM 315r 2018-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 3 47.8765 99.6 0.141 0.995 8.52 4.3 40636 67.3761830965
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 3 3.11 0.984 0.858
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 3.00081756367 47.8765 1.97481947278 40531 2001 99.6214821187 0.2213620728 0.219453008919 0.2215 0.258952836435 0.2593 87.9542643825
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 25.4332604169 f_angle_d 0.522231101943 f_chiral_restr 0.0388271642391 f_bond_d 0.00293437857648 f_plane_restr 0.002719322033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7504 Nucleic Acid Atoms 1020 Solvent Atoms 21 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing