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Crystal structure determination of uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans in complex with DNA - new insights into the role of the Leucine-loop for damage recognition and repair
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BOO PDB ENTRY 2BOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.05M NACITRATE, PH4.6 20%(W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.51 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.3 α = 90 b = 98.72 β = 90 c = 43.94 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2011-07-01 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 1.35 30 95.7 0.04 13 4.4 78013
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 1.35 1.38 91.7 0.6 2.15 4.4
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BOO 1.35 27.03 74096 3916 95.66 0.1838 0.18241 0.2125 0.21083 0.2352 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.245 r_dihedral_angle_4_deg 14.369 r_dihedral_angle_3_deg 11.405 r_rigid_bond_restr 8.999 r_dihedral_angle_1_deg 6.015 r_sphericity_bonded 4.297 r_long_range_B_refined 1.768 r_angle_refined_deg 1.719 r_long_range_B_other 1.683 r_scangle_other 1.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.245 r_dihedral_angle_4_deg 14.369 r_dihedral_angle_3_deg 11.405 r_rigid_bond_restr 8.999 r_dihedral_angle_1_deg 6.015 r_sphericity_bonded 4.297 r_long_range_B_refined 1.768 r_angle_refined_deg 1.719 r_long_range_B_other 1.683 r_scangle_other 1.583 r_scbond_it 1.462 r_scbond_other 1.462 r_angle_other_deg 1.175 r_mcangle_it 1.088 r_mcangle_other 1.087 r_mcbond_it 0.978 r_mcbond_other 0.977 r_chiral_restr 0.24 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1829 Nucleic Acid Atoms 457 Solvent Atoms 240 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing