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Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing an abasic site analog at the target base partner position
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G38 PDB ENTRY 1G38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 3 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.89 α = 90 b = 69.63 β = 90 c = 114.37 γ = 90
Symmetry Space Group P 21 21 21
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 4 ID14-3 (mirror) 2005-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 19.83 97.7 0.082 0.082 12.54 4.31 45098 44043 23.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 96.6 0.427 0.427 3.4 4.37 6656
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT PDB ENTRY 1G38 1.8 19.82 45053 44043 2203 97.76 0.16329 0.16123 0.1602 0.20196 0.1992 RANDOM 19.69
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] -1.54 1.56 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.52 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 12.89 r_dihedral_angle_1_deg 6.292 r_scangle_it 3.087 r_scbond_it 1.982 r_angle_refined_deg 1.479 r_mcangle_it 1.335 r_mcbond_it 0.892 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.52 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 12.89 r_dihedral_angle_1_deg 6.292 r_scangle_it 3.087 r_scbond_it 1.982 r_angle_refined_deg 1.479 r_mcangle_it 1.335 r_mcbond_it 0.892 r_nbtor_refined 0.31 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.131 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 3161 Nucleic Acid Atoms 396 Solvent Atoms 606 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement ProDC data collection MAR345 data collection XDS data scaling MOLREP phasing