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Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 PEG 4000, HEPES, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.605 α = 90 b = 44.399 β = 106.4 c = 81.516 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 110 CCD ADSC QUANTUM 210 2002-01-11 M 2 1 x-ray 110 CCD CUSTOM-MADE 2002-07-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9450 CHESS A1 2 SYNCHROTRON NSLS BEAMLINE X12C 1.0000, 0.9686, 1.0083 NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2,1 1.64 50 99.9 0.099 21.8 8.1 60643 60643 19.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.64 1.71 99.7 0.337 4.3 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.64 24.41 57518 57518 3124 99.94 0.15301 0.15126 0.18517 0.1892 RANDOM 22.947
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] 0.2 -0.32 0.26 -0.64
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.847 r_dihedral_angle_1_deg 4.932 r_scbond_it 4.799 r_mcangle_it 3.065 r_mcbond_it 1.943 r_angle_refined_deg 1.602 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.163 r_chiral_restr 0.16 r_symmetry_hbond_refined 0.14
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.847 r_dihedral_angle_1_deg 4.932 r_scbond_it 4.799 r_mcangle_it 3.065 r_mcbond_it 1.943 r_angle_refined_deg 1.602 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.163 r_chiral_restr 0.16 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3474 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing