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Crystal Structure of dnaN DNA polymerase III beta subunit from Stenotrophomonas maltophilia K279a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 MORPHEUS F5 (321505f5): 100 mM MOPS/HEPES-Na pH 7.5, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20mM D-xylose, 20 mM N-acetyl-D-glucosamine, 10% (w/v) PEG 20000, 20% (v/v) PEG MME 550, 16.74 mg/mL StmaA.17987.a.B1.PS38645, direct cryo
Crystal Properties Matthews coefficient Solvent content 3.24 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.96 α = 90 b = 160.96 β = 90 c = 36.15 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 RAYONIX MX-300 Beryllium Lenses 2021-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.15 46.47 99.9 0.078 0.087 0.999 16.99 5.009 29740 35.981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 100 0.586 0.655 0.841 2.94 5.021
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 4tsz 2.15 46.47 1.35 29735 2078 99.93 0.1719 0.1683 0.17 0.2205 0.2197 35.6982
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2825 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction