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Structure of human DNMT2 with bound competitive inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 Crystallization reservoir: 1.7 M ammonium sulfate, 9 % v/v glycerol, 0.117 M glycine pH 9.
Protein sample at 5 mg/mL.
Crystallization drops contained 300nL reservoir and 300 nL sample.
Crystals were grown at 291.15 K.
Crystal Properties Matthews coefficient Solvent content 2.98 58.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.537 α = 90 b = 116.537 β = 90 c = 69.826 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2023-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.8 41.77 100 0.103 0.042 0.999 14.3 13.8 43400 27.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 1.402 0.562 0.801 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 41.77 1.34 43370 2233 99.95 0.1642 0.1627 0.1627 0.1902 0.19 32.3
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.2585 f_angle_d 0.9118 f_chiral_restr 0.0557 f_bond_d 0.0082 f_plane_restr 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2546 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing