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Structure of human DNMT2, an enigmatic DNA methyltransferase homologue
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 289 1.3-1.4 M ammonium sulfate, 8 % glycerol, 100 mM glycine-NaOH pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.5 α = 90 b = 116.5 β = 90 c = 69.8 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 95 CCD BRANDEIS 2 1 x-ray IMAGE PLATE RIGAKU RAXIS IV M MAD 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.98 NSLS X12C 2 SYNCHROTRON NSLS BEAMLINE X12C 0.95189, 0.950051 NSLS X12C 3 ROTATING ANODE RIGAKU RU200 1.54
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 2 1.8 20 96.8 0.051 16.4 3.5 41963 146987
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 1.8 1.83 93.2 0.206 3.74 1976
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR 1.8 20 37121 1883 0.21 0.25 5% of total reflection (Random) 0.943
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 x_dihedral_angle_d 23.4 x_angle_d 1.5 x_improper_angle_d 1.4 x_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2474 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 41
Software Software Software Name Purpose PHASES phasing X-PLOR refinement DENZO data reduction SCALEPACK data scaling