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Crystal Structure of Vaccinia Virus Uracil DNA Glycosylase R187V Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OWQ PDB ENTRY 2OWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 1.5M Ammonium sulfate, 0.1M Hepes , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.195 α = 90 b = 85.195 β = 90 c = 139.439 γ = 120
Symmetry Space Group P 32 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 90 IMAGE PLATE RIGAKU RAXIS IV 2010-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.4 20 89.7 0.056 20.1 5.5 21064
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 2.4 2.44 94 0.34 5.2
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 2OWQ 2.4 20 19959 1103 89.62 0.22443 0.22164 0.2174 0.27402 0.2678 RANDOM 41.226
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] -0.22 -0.11 -0.22 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_3_deg 14.73 r_dihedral_angle_4_deg 13.489 r_dihedral_angle_1_deg 5.841 r_scangle_it 1.415 r_angle_refined_deg 1.118 r_scbond_it 0.854 r_mcangle_it 0.633 r_mcbond_it 0.335 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_3_deg 14.73 r_dihedral_angle_4_deg 13.489 r_dihedral_angle_1_deg 5.841 r_scangle_it 1.415 r_angle_refined_deg 1.118 r_scbond_it 0.854 r_mcangle_it 0.633 r_mcbond_it 0.335 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3483 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 22
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection DENZO data reduction