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Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 16-18% PEG 3350, 7.5, 50 mM Imidazole, 350 mM Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.643 α = 90 b = 80.158 β = 107.89 c = 55.251 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944 Viramax 2018-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.09 50 92.2 0.065 0.077 0.042 15 2.9 22805
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 2.1 2.14 41.2 0.208 0.278 0.182 0.868 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.094 21.982 1.34 22189 1952 89.48 0.2036 0.1985 0.2019 0.2556 0.2551 40.3725
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 21.284 f_angle_d 0.964 f_chiral_restr 0.052 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2611 Nucleic Acid Atoms 628 Solvent Atoms 234 Heterogen Atoms 39
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing