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Structure of Dnmt3a-Dnmt3L C-terminal domain complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PV0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 300 The final protein solution CONTAINED ~100 TO 133 micro M COMPLEX IN 20 milli M TRIS/HCL, PH 8.0, 100 milli M NACL, 5 % GLYCEROL, AND 0.1 % MERCAPTOETHANOL. Crystals were obtained with the mother liquor containing 2~5 % PEG 3000, 100 mM Tris/HCl, pH 8.0, 5 % glycerol at 16C, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.18 61.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 401.881 α = 90 b = 401.881 β = 90 c = 49.689 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 173 CCD MARMOSAIC 300 mm CCD 2006-04-06 M SINGLE WAVELENGTH 2 1 x-ray 173 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0, 0.9792, 0.9785,0.9719 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.89 40 100 0.058 14.8 3.2 65264 65264 -3 85.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.89 2.99 92.1 0.488 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT 2PV0 2.89 38.9 2 65264 54424 2756 81.9 0.259 0.259 0.259 0.2712 0.281 0.2868 RANDOM 101.3
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] 9.92 24.85 9.92 -19.84
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 9.07 c_mcangle_it 7.65 c_scbond_it 6.4 c_mcbond_it 4.84 c_angle_deg 1.4 c_improper_angle_d 1.04 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14557 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 104
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing