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Crystal structure of Uracil DNA-glycosylase from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUG PDB ENTRY 1EUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 50 MM MES AT PH 6.0. 28% (W/V) POLYETHYLENE GLYCOL (PEG) 3350.
Crystal Properties Matthews coefficient Solvent content 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.14 α = 90 b = 60.44 β = 90 c = 61.33 γ = 90
Symmetry Space Group P 21 21 21
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 2006-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.5 12 99.7 0.08 12.5 3.9 36324 11.81
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 1.5 1.58 100 0.48 2.9 3.9
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 1EUG 1.5 15.31 34471 1810 99.5 0.177 0.175 0.1755 0.21 0.2087 RANDOM 12.75
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] -0.31 -0.34 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.974 r_dihedral_angle_4_deg 15.813 r_dihedral_angle_3_deg 11.024 r_dihedral_angle_1_deg 5.757 r_scangle_it 2.967 r_scbond_it 1.881 r_angle_refined_deg 1.329 r_mcangle_it 1.148 r_mcbond_it 0.719 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.974 r_dihedral_angle_4_deg 15.813 r_dihedral_angle_3_deg 11.024 r_dihedral_angle_1_deg 5.757 r_scangle_it 2.967 r_scbond_it 1.881 r_angle_refined_deg 1.329 r_mcangle_it 1.148 r_mcbond_it 0.719 r_nbtor_refined 0.31 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 1777 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing