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Crystal structure of Sulfolobus solfataricus 8-oxoguanine DNA glycosylase (SsOgg)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FHF PDB entry 3FHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 285 50 mM sodium cacodylate, 2M (NH4)2SO4, 10mM MgSO4, (from four years old crystal tray), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.96 α = 90 b = 110.96 β = 90 c = 34.41 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 CCD MARMOSAIC 300 mm CCD Adjustable focus K-B pair Si plus Pt, Rh coatings 2008-03-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9794 APS 23-ID-B
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 1.9 20 95.9 0.085 0.06 17.6 5.7 37393 37358 24.1
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 1.9 2 100 0.536 0.696 2.3 5.7 5344
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 THROUGHOUT PDB entry 3FHF 1.9 19.7 37350 35849 1902 99.9 0.224 0.226 0.207 0.2133 0.248 0.2547 RANDOM 33.084
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] 1.84 1.84 -3.69
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.7 c_scangle_it 3.06 c_scbond_it 2.08 c_mcangle_it 1.87 c_mcbond_it 1.28 c_angle_deg 1.1 c_improper_angle_d 0.7 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1707 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 80
Software Software Software Name Purpose XSCALE data processing CNS refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction XSCALE data scaling MOLREP phasing