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Crystal structure of a predicted N6-adenine-specific DNA methylase from Listeria monocytogenes str. 4b F2365
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.2 M Ammonium sulfate
25 % PEG3350
0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.949 α = 90 b = 46.156 β = 131.09 c = 91.376 γ = 90
Symmetry Space Group C 1 2 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 315r mirrors 2009-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.5 40 98 0.058 32 3 63435 62193 2 2 29
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 1.5 1.53 95.6 0.52 2.1 2.9 3036
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 SAD THROUGHOUT 1.5 40 2 2 62195 59033 3160 97.74 0.17 0.16591 0.16417 0.1843 0.19771 0.2145 RANDOM 9.691
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] 1.24 0.92 -0.89 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.363 r_dihedral_angle_4_deg 17.737 r_dihedral_angle_3_deg 12.684 r_dihedral_angle_1_deg 5.859 r_scangle_it 4.638 r_scbond_it 2.961 r_mcangle_it 1.779 r_angle_refined_deg 1.625 r_mcbond_it 1.026 r_angle_other_deg 0.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.363 r_dihedral_angle_4_deg 17.737 r_dihedral_angle_3_deg 12.684 r_dihedral_angle_1_deg 5.859 r_scangle_it 4.638 r_scbond_it 2.961 r_mcangle_it 1.779 r_angle_refined_deg 1.625 r_mcbond_it 1.026 r_angle_other_deg 0.984 r_mcbond_other 0.318 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2998 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 10
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELX model building DM model building ARP/wARP model building Coot model building CCP4 model building MLPHARE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing DM phasing CCP4 phasing