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Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YG8 PDB ENTRY 2YG8
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 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.311 α = 90 b = 51.372 β = 99.71 c = 90.039 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 MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.95 42.68 99.8 0.14 8.8 4.1 35790 12.76
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 1.95 2.06 99.8 0.48 3 4.2
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YG8 1.95 42.68 33988 1802 99.77 0.17315 0.17011 0.1773 0.23101 0.2342 RANDOM 9.348
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] 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.507 r_dihedral_angle_4_deg 16.673 r_dihedral_angle_3_deg 14.195 r_dihedral_angle_1_deg 4.817 r_scangle_it 3.528 r_scbond_it 2.343 r_angle_refined_deg 1.476 r_mcangle_it 1.28 r_angle_other_deg 1.017 r_mcbond_it 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.507 r_dihedral_angle_4_deg 16.673 r_dihedral_angle_3_deg 14.195 r_dihedral_angle_1_deg 4.817 r_scangle_it 3.528 r_scbond_it 2.343 r_angle_refined_deg 1.476 r_mcangle_it 1.28 r_angle_other_deg 1.017 r_mcbond_it 1.013 r_symmetry_vdw_other 0.323 r_symmetry_vdw_refined 0.259 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.213 r_mcbond_other 0.212 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.176 r_chiral_restr 0.09 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 612 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing