☰ Navigation Tabs
Crystal structure of DNA polymerase III subunit beta from Rickettsia rickettsii
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 5.6 290 Rigaku Reagents Top96 G6: (0.5 M Ammonium Sulfate, 0.1 M Sodium Citrate:Citric Acid pH 5.6, 1 M Lithium Sulfate) mixed 1:1 with 20 mg/mL protein in sitting drop vapor diffusion. Tray id 291006g9, crystal id qtv9-3
Crystal Properties Matthews coefficient Solvent content 2.66 53.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.09 α = 90 b = 97.57 β = 90 c = 115.83 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r Beryllium Lenses 2017-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.97872 ALS 8.2.1
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 36.649 99.6 0.056 0.061 0.999 22.18 6.037 60964 30.5
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 2.05 100 0.584 0.644 0.845 3.1 5.648
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 36.649 1.34 60951 1976 99.55 0.168 0.1666 0.169 0.2116 0.2155
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 13.758 f_angle_d 1.201 f_chiral_restr 0.082 f_bond_d 0.015 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5713 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing