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Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UI1 Selenomethionyl uracil-DNA glycosylase from Thermus thermophilus HB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 1.2-1.5M ammonium sulfate, 75mM Tris, 25% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.429 α = 90 b = 59.512 β = 90 c = 80.971 γ = 90
Symmetry Space Group P 21 21 21
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 V 2002-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.98 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 48.2 99.9 35830 10.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 99.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Selenomethionyl uracil-DNA glycosylase from Thermus thermophilus HB8 1.5 10 35638 3543 99.6 0.183 0.183 0.176 0.201 0.1946 RANDOM 11.2
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] -2.73 0.39 2.34
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 2.51 c_scbond_it 1.7 c_mcangle_it 1.41 c_angle_deg 1.2 c_improper_angle_d 1.18 c_mcbond_it 0.93 c_bond_d 0.004 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 2.51 c_scbond_it 1.7 c_mcangle_it 1.41 c_angle_deg 1.2 c_improper_angle_d 1.18 c_mcbond_it 0.93 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 29
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing