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Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1 UL DROPS OF 10 MG/ML PROTEIN MIXED WITH A SOLUTION CONTAINING 1 M LICL2, 0.1 M MES PH 6.0 AND 10% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.562 α = 90 b = 51.297 β = 99.76 c = 90.458 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 CCD TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 49.75 100 0.12 14.8 6.3 33423 12.7
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 2.11 100 0.39 5.1 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 SAD THROUGHOUT NONE 2 49.75 31731 1693 99.98 0.16054 0.15828 0.166 0.20315 0.2082 RANDOM 8.644
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] 0.04 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_4_deg 17.396 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 4.866 r_scangle_it 3.84 r_scbond_it 2.567 r_angle_refined_deg 1.43 r_mcangle_it 1.312 r_angle_other_deg 1.065 r_mcbond_it 1.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_4_deg 17.396 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 4.866 r_scangle_it 3.84 r_scbond_it 2.567 r_angle_refined_deg 1.43 r_mcangle_it 1.312 r_angle_other_deg 1.065 r_mcbond_it 1.002 r_symmetry_vdw_other 0.283 r_mcbond_other 0.216 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.211 r_nbd_other 0.2 r_nbtor_refined 0.173 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.146 r_nbtor_other 0.086 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3073 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SHARP phasing