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Crystal Structure of the DNMT3A ADD domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 17% PEG 8000, 0.1M Tris-HCl, 0.2M magnesium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.581 α = 90 b = 57.581 β = 90 c = 138.949 γ = 120
Symmetry Space Group P 61 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 315 mirrors 2007-10-19 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 mirrors 2007-10-19 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.28221, 1.28333, 1.25730, 1.29001 Photon Factory BL-5A
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 2.3 28.796 98.9 0.063 16.4 12.3 6567 6551 1 1
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) 1,2 2.3 2.38 99.2 0.41 12.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.3 28.79 6245 306 99.42 0.21113 0.20938 0.2044 0.24968 0.2429 RANDOM 45.477
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] 0.17 0.09 0.17 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 20.497 r_dihedral_angle_3_deg 16.831 r_dihedral_angle_1_deg 6.224 r_scangle_it 1.999 r_scbond_it 1.419 r_angle_refined_deg 1.316 r_mcangle_it 0.825 r_mcbond_it 0.463 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 20.497 r_dihedral_angle_3_deg 16.831 r_dihedral_angle_1_deg 6.224 r_scangle_it 1.999 r_scbond_it 1.419 r_angle_refined_deg 1.316 r_mcangle_it 0.825 r_mcbond_it 0.463 r_nbtor_refined 0.302 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.193 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1035 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing