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Structures of Vaccinia Virus Uracil-DNA Glycosylase in New Crystal Forms
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, 10% Glycerol, 0.1M Hepes, 10mM Nickel sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.79 α = 90 b = 85.79 β = 90 c = 123.46 γ = 120
Symmetry Space Group P 64 2 2
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 2010-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.3 19.93 92.8 0.067 0.067 12.8 3.7 11573 11573 42
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 2.3 2.38 94 0.369 0.369 3.7 3.7 2322
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 (All) 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 2.3 19.55 11016 11016 555 92.42 0.23623 0.23623 0.23431 0.2331 0.27573 0.2748 RANDOM 51.731
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] -1.35 -0.67 -1.35 2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.496 r_dihedral_angle_3_deg 15.442 r_dihedral_angle_4_deg 7.25 r_dihedral_angle_1_deg 5.888 r_angle_refined_deg 1.139 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1741 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 9
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling