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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 2-aminopurine at the target position and 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 (10mM Tris/HCl, 300mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100mM KCl, 100mM MgCl2, 6% isopropanol, 50mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.339 α = 90 b = 68.699 β = 92.09 c = 114.022 γ = 90
Symmetry Space Group P 1 21 1
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 mirror 2005-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.9310 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 1.7 19.92 98 0.077 0.077 11.51 3.8 100843 98855 23.22
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 1.7 1.8 97.3 0.38 0.38 3.65 3.76 15379
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 (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 PDB ENTRY 1G38 1.7 19.92 100769 98855 4943 98.1 0.1687 0.1687 0.16687 0.1653 0.20322 0.2001 RANDOM 17.313
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] -0.07 -0.07 0.5 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.992 r_dihedral_angle_4_deg 15.452 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.111 r_scangle_it 2.959 r_scbond_it 1.946 r_angle_refined_deg 1.459 r_mcangle_it 1.294 r_mcbond_it 0.822 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.992 r_dihedral_angle_4_deg 15.452 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.111 r_scangle_it 2.959 r_scbond_it 1.946 r_angle_refined_deg 1.459 r_mcangle_it 1.294 r_mcbond_it 0.822 r_nbtor_refined 0.31 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.091 r_bond_refined_d 0.011 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 6378 Nucleic Acid Atoms 792 Solvent Atoms 1041 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement ProDC data collection MAR345 data collection XDS data scaling MOLREP phasing