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Structure of mouse polymerase beta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287.15 0.1 M HEPES pH 7.5, 22.5% w/v PEG3350, 1.5% v/v Tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.32 86.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.725 α = 90 b = 120.534 β = 90 c = 69.043 γ = 90
Symmetry Space Group P 21 21 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 PIXEL Bruker PHOTON III Incoatec Microfocus Sources 3.0 2022-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS 3.0 MICROFOCUS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.647 34.726 100 0.082 0.088 0.031 0.999 20.4 8 63779 13.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.647 1.68 99.9 1.031 1.126 0.447 0.625 1.9 6.3
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 1ZQY 1.65 34.52 1.34 63706 6525 99.96 0.1775 0.1734 0.1731 0.2142 0.2128 17.41
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 13.4277 f_angle_d 1.0521 f_chiral_restr 0.0687 f_bond_d 0.0105 f_plane_restr 0.0103
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3872 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 14
Software Software Software Name Purpose APEX data collection PHENIX refinement PHENIX model building SAINT data reduction Aimless data scaling PHASER phasing