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Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine DNA glycosylase (MjOgg)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 285 PEG 4000 30%, 0.1M sodium citrate, 1% b-Mercaptoethanol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.21 44.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.44 α = 90 b = 37.84 β = 116.08 c = 75.01 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 300 mm CCD Adjustable focus K-B pair Si plus Pt, Rh coatings 2008-03-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9794, 0.9796, 0.97166 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 1.995 19.56 96.4 0.068 0.084 15.43 5.8 29750 28691 14.9
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 1.995 2.1 92.1 0.203 0.279 8.23 5.8 4041
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 THROUGHOUT 1.995 19.56 15485 15220 759 98.5 0.217 0.222 0.202 0.2082 0.251 0.2546 RANDOM 24.682
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] -3.22 0.39 4.18 -0.96
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.2 c_scangle_it 3.42 c_scbond_it 2.33 c_mcangle_it 1.89 c_mcbond_it 1.31 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 1815 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose SCALA data processing CNS refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction SCALA data scaling SHARP phasing