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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 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.46 α = 90 b = 120.46 β = 90 c = 50.1 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 2006-02-07 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 2.5 19.72 97.3 0.132 0.132 5.7 2.8 14156 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) 2.5 2.59 95 0.346 0.346 2.7 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 2OKD 2.5 13.47 13164 13164 694 95.8 0.222 0.22 0.2314 0.274 0.2765 RANDOM 20.37
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 0.15 0.31 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.093 r_dihedral_angle_4_deg 18.825 r_dihedral_angle_3_deg 14.787 r_dihedral_angle_1_deg 4.99 r_scangle_it 1.24 r_angle_refined_deg 1.058 r_scbond_it 0.663 r_mcangle_it 0.399 r_nbtor_refined 0.308 r_mcbond_it 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.093 r_dihedral_angle_4_deg 18.825 r_dihedral_angle_3_deg 14.787 r_dihedral_angle_1_deg 4.99 r_scangle_it 1.24 r_angle_refined_deg 1.058 r_scbond_it 0.663 r_mcangle_it 0.399 r_nbtor_refined 0.308 r_mcbond_it 0.217 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.151 r_symmetry_vdw_refined 0.145 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.06 r_bond_refined_d 0.006 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 2889 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing