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Native Structure of the Human 8-oxoguanine DNA Glycosylase hOGG1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EBM PDB entry 1EBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 277 PEG 4000, Ammonium Sulphate, Sodium citrate, pH 4.6, Microbatch, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.97 37.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.513 α = 90 b = 105.513 β = 90 c = 47.597 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 MARRESEARCH Sagitally focussing Ge (220) and a multilayer 1999-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 2.15 25 99.9 0.04 0.04 13.4 3.8 17927 17891 2 2 23.4
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) 2.15 2.27 99.9 0.215 0.215 3.5 3.8 2402
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1EBM 2.15 23.07 17891 17891 832 99.9 0.21 0.21 0.206 0.252 RANDOM 33.4
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] 0.65 2.69 0.65 -1.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 3.24 c_scbond_it 2.24 c_mcangle_it 2.2 c_mcbond_it 1.41 c_angle_deg 1.1 c_improper_angle_d 0.85 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2445 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 10
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling