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Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing cytosine opposite to 8-oxoG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 277 PEG-4000 16%, 0.1M NaAcetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.4 α = 90 b = 92.4 β = 90 c = 191.05 γ = 120
Symmetry Space Group P 65 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 CCD MAR345 2009-01-09 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 1.73 19.9 94.7 0.056 0.06 32.2 14.2 51091 48375 20.7
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) 1.73 1.8 79.2 0.325 0.566 4.93 11.1
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 3F0Z 1.73 19.9 51091 48375 2444 95 0.195 0.195 0.2032 0.219 0.2242 RANDOM 27.3
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] 0.73 0.73 -1.45
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 2.87 c_scbond_it 1.86 c_mcangle_it 1.6 c_angle_deg 1.1 c_mcbond_it 1.09 c_improper_angle_d 0.81 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 2.87 c_scbond_it 1.86 c_mcangle_it 1.6 c_angle_deg 1.1 c_mcbond_it 1.09 c_improper_angle_d 0.81 c_bond_d 0.005 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 2454 Nucleic Acid Atoms 508 Solvent Atoms 319 Heterogen Atoms 21
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction