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The crystal structure of Uracil-DNA N-Glycosylase (UNG) from Deinococcus radiodurans.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKZ PDB ENTRY 1AKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 0.2 M AMMONIUM NITRATE, 17% (W/V) PEG 3000 AT 4 DEGREES C, pH 7.50
Crystal Properties Matthews coefficient Solvent content 4.1 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.5 α = 90 b = 85.1 β = 90 c = 85.9 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 CCD MARRESEARCH TOROIDAL MIRROR 2003-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.8 28.36 93.7 0.1 4.44 2.52 40425 20
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 1.8 1.9 95.2 0.27 2.65 2.37
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 1AKZ 1.8 84.52 38387 2038 92.6 0.236 0.234 0.2411 0.272 0.2763 RANDOM 23.19
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] -2.37 -2.59 4.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.573 r_dihedral_angle_3_deg 17.264 r_dihedral_angle_4_deg 14.976 r_dihedral_angle_1_deg 6.913 r_scangle_it 4.205 r_scbond_it 3.966 r_mcbond_it 1.965 r_angle_refined_deg 1.841 r_mcangle_it 1.727 r_angle_other_deg 1.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.573 r_dihedral_angle_3_deg 17.264 r_dihedral_angle_4_deg 14.976 r_dihedral_angle_1_deg 6.913 r_scangle_it 4.205 r_scbond_it 3.966 r_mcbond_it 1.965 r_angle_refined_deg 1.841 r_mcangle_it 1.727 r_angle_other_deg 1.002 r_symmetry_vdw_other 0.262 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.207 r_nbtor_refined 0.186 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.111 r_nbtor_other 0.089 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.002 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_mcbond_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 1839 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing