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X-ray diffraction data of DNA Polymerase Eta (RAD30) of Saccharomyces cerevisiae with a single magnesium bound in absence of DNA and incoming dNTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 20% v/v Glycerin (Additive), 14.4% w/v PEG 8000 (Precipitant), 0.08 M NaCac 6.5 pH (Buffer), 0.16 M Ca(OAc)2 (Salt)
Crystal Properties Matthews coefficient Solvent content 3.99 69.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.681 α = 90 b = 130.681 β = 90 c = 93.908 γ = 120
Symmetry Space Group P 31 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 NOIR-1 2017-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.8 56.587 100 0.096 0.105 0.032 18.8 10.6 23171 23171 69.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 1.024 1.024 1.126 0.343 0.8 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1JIH 2.8 43.37 1.32 23171 2264 99.96 0.2223 0.2208 0.2295 0.249 0.2541 79.644
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.139 f_angle_d 0.619 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3957 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction SCALA data scaling PHASER phasing Coot model building