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Crystal structure of DNMT3B-DNMT3L in complex with CpGpA 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 8 289.15 0.1 M Tris-HCl (pH 8.0), 100 mM MgCl2, 7% PEG8000
Crystal Properties Matthews coefficient Solvent content 4.28 71.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.303 α = 90 b = 193.303 β = 90 c = 49.649 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 2018-11-06 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) Rrim I (All) 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 3.04308940064 50 100 0.13 0.149 0.071 4.5 4.3 39794
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.16 100 0.833 0.963 0.477 0.838 4
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 3.05 48.32575 1.97543196468 39736 2027 99.8417045654 0.209463676788 0.207908654931 0.2083 0.239110006433 0.2399 90.6118931347
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 19.2177411316 f_angle_d 0.631208885056 f_chiral_restr 0.0404655722575 f_plane_restr 0.00447712929687 f_bond_d 0.00381259273705
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7377 Nucleic Acid Atoms 1025 Solvent Atoms 38 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing