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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 1Q5U PDB ENTRY 1Q5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 298 12% PEG1000, 0.1M lithium sulfate, 0.1M phosphate/citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.20
Crystal Properties Matthews coefficient Solvent content 2.09 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.26 α = 90 b = 105.26 β = 90 c = 59.29 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 2005-06-05 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 2.15 49.7 98.6 0.033 0.033 29.9 6.2 20238 1 27
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 2.15 2.23 92.1 0.144 0.144 6 2.6
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 1Q5U 2.15 18.13 19126 19126 1034 98.4 0.212 0.21 0.2267 0.257 0.2637 RANDOM 30.84
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] 0.03 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.801 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 11.892 r_dihedral_angle_1_deg 5.671 r_scangle_it 1.101 r_angle_refined_deg 0.902 r_scbond_it 0.697 r_mcangle_it 0.548 r_mcbond_it 0.31 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.801 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 11.892 r_dihedral_angle_1_deg 5.671 r_scangle_it 1.101 r_angle_refined_deg 0.902 r_scbond_it 0.697 r_mcangle_it 0.548 r_mcbond_it 0.31 r_nbtor_refined 0.309 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.116 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 2643 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing