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High Resolution Crystal Structures of Vaccinia Virus dUTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OKD PDB ENTRY 2OKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 20% PEG2000 MME, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.66 α = 90 b = 119.66 β = 90 c = 50.16 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2006-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 19.94 99.5 0.078 0.078 10.2 3.6 24014 1 23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 99 0.347 0.347 3.4 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2OKD 2.1 19.58 22718 22718 1156 99.6 0.209 0.207 0.2167 0.261 0.2662 RANDOM 24.55
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 30.469 r_dihedral_angle_4_deg 21.186 r_dihedral_angle_3_deg 14.437 r_dihedral_angle_1_deg 5.967 r_scangle_it 1.698 r_angle_refined_deg 1.188 r_scbond_it 1.022 r_mcangle_it 0.599 r_mcbond_it 0.348 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.469 r_dihedral_angle_4_deg 21.186 r_dihedral_angle_3_deg 14.437 r_dihedral_angle_1_deg 5.967 r_scangle_it 1.698 r_angle_refined_deg 1.188 r_scbond_it 1.022 r_mcangle_it 0.599 r_mcbond_it 0.348 r_nbtor_refined 0.31 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2915 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing