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Post catalytic complex of Prim-PolC from Mycobacterium smegmatis with gapped DNA and 3'-dUTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 285 50mM Sodium cacodylate, 2M Ammonium sulphate, 10mM Manganese Chloride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.25 α = 90 b = 198.25 β = 90 c = 85.3 γ = 90
Symmetry Space Group P 4 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 DECTRIS PILATUS 6M KB bimorph mirror pair 2017-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 2.01 99.12 100 0.047 0.051 0.02 0.999 20 6.4 112811 44.314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.04 100 1.423 0.594 1.2 5.6
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 THROUGHOUT 5OP0 2.01 88.66 1.34 112714 5636 99.91 0.1855 0.1845 0.1908 0.2042 0.2128 73.5611
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 20.458 f_angle_d 1.016 f_chiral_restr 0.059 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5198 Nucleic Acid Atoms 1099 Solvent Atoms 362 Heterogen Atoms 173
Software Software Software Name Purpose DIALS data reduction xia2 data scaling PHASER phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction