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Crystal structure of vaccinia virus uracil-DNA glycosylase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.25 295 1.5 M ammonium sulfate, 12% glycerol, 0.1M Hepes, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.197 α = 90 b = 85.197 β = 90 c = 139.725 γ = 120
Symmetry Space Group P 32 2 1
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 Osmic Mirrors 2005-10-02 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 2.4 19.96 98.6 0.061 0.061 11 2.68 23203 23203 1 1 35
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 2.48 99.5 0.299 0.299 3.4 2.65
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SIRAS THROUGHOUT 2.4 19.27 23150 21956 1194 98.44 0.2436 0.2436 0.2407 0.2365 0.2995 0.2882 RANDOM 27.54
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] -0.06 -0.03 -0.06 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.082 r_dihedral_angle_4_deg 16.18 r_dihedral_angle_3_deg 15.974 r_dihedral_angle_1_deg 6.044 r_angle_refined_deg 1.127 r_scangle_it 0.832 r_scbond_it 0.509 r_mcangle_it 0.463 r_nbtor_refined 0.304 r_mcbond_it 0.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.082 r_dihedral_angle_4_deg 16.18 r_dihedral_angle_3_deg 15.974 r_dihedral_angle_1_deg 6.044 r_angle_refined_deg 1.127 r_scangle_it 0.832 r_scbond_it 0.509 r_mcangle_it 0.463 r_nbtor_refined 0.304 r_mcbond_it 0.265 r_symmetry_vdw_refined 0.242 r_symmetry_hbond_refined 0.239 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3514 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement StructureStudio data collection d*TREK data reduction d*TREK data scaling SHELXS phasing