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Crystal structure of DNMT3A-DNMT3L complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QRV 2QRV, 3A1A experimental model PDB 3A1A 2QRV, 3A1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 291 0.05M Bis-Tris, 0.1M Sodium Malonate, 8% PEG3350
Crystal Properties Matthews coefficient Solvent content 4.46 72.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 252.031 α = 90 b = 252.031 β = 90 c = 75.336 γ = 120
Symmetry Space Group P 63 2 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 CCD ADSC QUANTUM 315r 2013-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.2816 SSRF BL17U
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 3.82 50 99.9 0.098 0.108 0.046 6.9 5.7 14153 46.31
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 3.82 3.96 99.9 0.87 0.958 0.397 0.688 5.8 1378
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2QRV, 3A1A 3.821 42.005 1.33 13977 1392 79.18 0.2285 0.224 0.2459 0.2688 0.2827 Random selection 78.3298
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 14.243 f_angle_d 0.977 f_chiral_restr 0.036 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5043 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data collection HKL-2000 data scaling PHASER model building