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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 2OKB PDB ENTRY 2OKB
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 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.01 α = 90 b = 120.01 β = 90 c = 50.3 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 2005-11-05 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 2.4 50 98.3 0.134 0.134 6.8 3.1 16130 1 31
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 2.4 2.49 97.3 0.423 0.423 1.2 2.7
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 2OKB 2.4 19.64 14683 14683 753 97.5 0.209 0.206 0.209 0.268 0.2676 RANDOM 31.68
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 32.271 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 14.41 r_dihedral_angle_1_deg 5.997 r_scangle_it 1.294 r_angle_refined_deg 1.011 r_scbond_it 0.751 r_mcangle_it 0.549 r_nbtor_refined 0.308 r_mcbond_it 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.271 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 14.41 r_dihedral_angle_1_deg 5.997 r_scangle_it 1.294 r_angle_refined_deg 1.011 r_scbond_it 0.751 r_mcangle_it 0.549 r_nbtor_refined 0.308 r_mcbond_it 0.3 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.064 r_bond_refined_d 0.007 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 2911 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing